pipeline.yaml

__pipeline__:
  name: phoenix
  main: main.jst
  description: Human GRCh38 genomics suite
  version: v1.2.0
constants:
  tools:
    bedtools:
      module: BEDTools/2.29.0-GCC-8.2.0-2.31.1
      version: "2.29.0"
      verbose: BEDTools v2.29.0
      website: https://bedtools.readthedocs.io/
      citation: >
        Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing
        genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi:
        10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed
        Central PMCID: PMC2832824.
    bcftools:
      module: BCFtools/1.10.2-GCC-8.2.0-2.31.1
      version: "1.10.2"
      verbose: BCFtools v1.10.2
      website: http://www.htslib.org
      citation: >
        TODO
    bowtie2:
      module: Bowtie2/2.3.5.1-GCC-8.2.0-2.31.1
      version: "2.3.5.1"
      verbose: bowtie2 v2.3.5.1
      website: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
      citation: >
        TODO
    bwa:
      module: BWA/0.7.17-GCC-8.2.0-2.31.1
      version: "0.7.17"
      verbose: Burrows-Wheeler Aligner v0.7.17
      website: http://bio-bwa.sourceforge.net
      citation: >
        Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform.
        Bioinformatics, 25:1754-60. [PMID: 19451168]
    bwa_mem2:
      module: bwa-mem2/2.2.1
      version: "2.2.1"
      verbose: Burrows-Wheeler Aligner v2.2.1
    cellranger:
      module: cellranger/6.0.1
      version: "6.0.1"
      verbose: 10X CellRanger v6.0.1
      website: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
      citation: >
        TODO
    cuda_toolkit:
      module: CUDA/10.1.243
      version: "10.0.0"
      verbose: NVIDIA CUDA 10.0
      website: https://developer.nvidia.com/cuda-toolkit
    deepvariant:
      module: deepvariant/0.10.0-gpu-phoenix
      version: "0.10.0-gpu"
      verbose: DeepVariant 0.10.0-gpu
      website: https://github.com/google/deepvariant
      citation: >
        Poplin R, Chang PC, Alexander D, Schwartz S, Colthurst T, Ku A, Newburger D,
        Dijamco J, Nguyen N, Afshar PT, Gross SS, Dorfman L, McLean CY, DePristo MA. A
        universal SNP and small-indel variant caller using deep neural networks. Nat
        Biotechnol. 2018 Nov;36(10):983-987. doi: 10.1038/nbt.4235. Epub 2018 Sep 24.
        PubMed PMID: 30247488.
    delly:
      module: Delly/0.7.6-linux_x86_64
      version: "0.7.6"
      verbose: DELLY2 v0.7.6
      website: https://github.com/dellytools/delly
      citation: >
        Tobias Rausch, Thomas Zichner, Andreas Schlattl, Adrian M. Stütz, Vladimir Benes, Jan O. Korbel,
        DELLY: structural variant discovery by integrated paired-end and split-read analysis, Bioinformatics,
        Volume 28, Issue 18, 15 September 2012, Pages i333–i339, https://doi.org/10.1093/bioinformatics/bts378
    dle:
      module: DLE/0.1.5
      version: "0.1.5"
      verbose: Discordant Loci Extractor v0.1.5
    expansion_hunter:
      module: ExpansionHunter/4.0.2
      version: "4.0.2"
      verbose: Illumina ExpansionHunter v4.0.2
      citation: >
        Egor Dolzhenko, Viraj Deshpande, Felix Schlesinger, Peter Krusche, Roman Petrovski, and others,
        ExpansionHunter: A sequence-graph based tool to analyze variation in short tandem repeat regions,
        Bioinformatics 2019
    freebayes:
      module: freebayes/1.3.1-foss-2019a
      version: "1.3.1"
      verbose: Freebayes v1.3.1
      website: https://github.com/ekg/freebayes
      citation: >
        Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing.
        arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012
    gatk:
      module: GATK/4.1.8.0-GCCcore-8.3.0-Java-1.8
      version: "4.1.8.0"
      verbose: Genome Analysis Toolkit v4.1.8.0
      website: https://software.broadinstitute.org/gatk/
      citation: >
        The Genome Analysis Toolkit: a MapReduce framework for analyzing
        next-generation DNA sequencing data McKenna A, Hanna M, Banks E,
        Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D,
        Gabriel S, Daly M, DePristo MA, 2010 GENOME RESEARCH 20:1297-303
    gridss:
      module: gridss/2.6.3
      version: "2.6.3"
      verbose: Genomic Rearrangement IDentification Software Suite v2.6.3
      website: https://github.com/PapenfussLab/gridss
      citation: >
        Daniel L. Cameron, Jan Schröder, Jocelyn Sietsma Penington, Hongdo Do,
        Ramyar Molania, Alexander Dobrovic, Terence P. Speed and Anthony T. Papenfuss.
        GRIDSS: sensitive and specific genomic rearrangement detection using positional
        de Bruijn graph assembly. Genome Research, 2017 doi: 10.1101/gr.222109.117
    hmmcopy_utils:
      module: HMMCopy_Utils/1.0.0-5911bf6
      version: "1.0"
      verbose: HMM Copy Utils v1.0
      website: https://github.com/shahcompbio/hmmcopy_utils
      citation: >
        Daniel Lai dalai@bccrc.ca Department of Molecular Oncology, BC Cancer
        Research Agency Date: August 02, 2011
    htslib:
      module: HTSlib/1.10.2-GCC-8.2.0-2.31.1
      version: "1.10.2"
      verbose: HTSlib v1.10.2
      website: http://www.htslib.org
      citation: >
        TODO
    htseq:
      module: HTSeq/0.12.3-foss-2018b-Python-3.6.6
      version: 0.12.3
      verbose: HTSeq v0.12.3
      website: https://htseq.readthedocs.io
      citation: >
        Simon Anders, Paul Theodor Pyl, Wolfgang Huber
        HTSeq — A Python framework to work with high-throughput sequencing data
        Bioinformatics (2014), in print, online at doi:10.1093/bioinformatics/btu638
    ichorcna:
      module: R/3.6.1-phoenix
      launcher: required_scripts/runIchorCNA_47ce8db.R
      version: "0.2.0"
      verbose: ichorCNA v0.2.0
      website: https://github.com/broadinstitute/ichorCNA
      citation: >
        Adalsteinsson, Ha, Freeman, et al. Scalable whole-exome sequencing of
        cell-free DNA reveals high concordance with metastatic tumors. (2017)
        Nature Communications Nov 6;8(1):1324. doi: 10.1038/s41467-017-00965-y
    lancet:
      module: lancet/1.1.x-GCC-8.2.0-2.31.1
      version: "1.1.x"
      verbose: lancet v1.1.x
      website: https://github.com/nygenome/lancet
      citation: >
        Narzisi G, Corvelo A, Arora K, Bergmann E, Shah M, Musunuri R, Emde AK, Robine N, Vacic V,
        Zody MC. Genome-wide somatic variant calling using localized colored de Bruijn graphs.
        Communications Biology, Nature Research publishing, volume 1, Article number: 20, 2018
        (DOI:10.1038/s42003-018-0023-9). Also available at CSHL bioRxiv 196311; 2017 (DOI: 10.1101/196311)
    lumosvar2:
      module: LumosVar2/1.1
      version: "1.1"
      verbose: LumosVar2 v1.1
      website: https://github.com/tgen/lumosVar2
      citation: >
        Joint analysis of matched tumor samples with varying tumor contents
        improves somatic variant calling in the absence of a germline sample.
        bioRxiv 364943; doi: https://doi.org/10.1101/364943
    manta:
      module: manta/1.6
      version: "1.6"
      verbose: Manta v1.6
      website: https://github.com/Illumina/manta
      citation: >
        Chen, X. et al. (2016) Manta: rapid detection of structural variants and indels for germline and
        cancer sequencing applications. Bioinformatics, 32, 1220-1222. doi:10.1093/bioinformatics/btv710
    manta_tgen:
      module: manta/1.6_tgen
      version: "1.6"
      verbose: Manta v1.6 tgen_fork
      website: https://github.com/tgen/manta
    msisensor:
      module: MSIsensor/1.1.a-GCCcore-8.2.0
      version: "1.1.a"
      verbose: MSIsensor v1.1.a
      website: https://github.com/xjtu-omics/msisensor-pro
    multiqc:
      module: Python/3.7.2-foss-2019a
      version: "1.9"
      verbose: MultiQC v1.9
      website: https://multiqc.info
      citation: >
        MultiQC Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
      doi: 10.1093/bioinformatics/btw354
      PMID: 27312411
    octopus:
      module: Octopus/0.6.3-beta-foss-2019a
      version: 0.6.3-beta
      verbose: Octopus v0.6.3-beta
      website: https://github.com/luntergroup/octopus
      citation: >
        A unified haplotype-based method for accurate and comprehensive variant calling Daniel P Cooke,
        David C Wedge, Gerton Lunter bioRxiv 456103; doi: https://doi.org/10.1101/456103
    openmpi:
      module: openmpi/3.1.3
      version: 3.1.3
      verbose: openmpi v3.1.3
      website: https://www-lb.open-mpi.org/software/ompi/v3.1/
      citation: >
        Open MPI: Goals, Concept, and Design of a Next Generation MPI Implementation. Edgar Gabriel,
        Graham E. Fagg, George Bosilca, Thara Angskun, Jack J. Dongarra, Jeffrey M. Squyres, Vishal Sahay,
        Prabhanjan Kambadur, Brian Barrett, Andrew Lumsdaine, Ralph H. Castain, David J. Daniel, Richard
        L. Graham, and Timothy S. Woodall. In Proceedings, 11th European PVM/MPI Users' Group Meeting,
        Budapest, Hungary, September 2004.
    pairoscope:
      module: pairoscope/0.4.2
      version: 0.4.2
      verbose: pairoscope v0.4.2
      website: https://github.com/genome/pairoscope
      citation: >
        TBD
    petagene:
      module: petagene/1.3.0p7
      version: 1.3.0p7
      PetaLinkMode: "+fastq"
    phaser:
      module: phASER/1.1.1-python-2.7.13
      version: 1.1.1
      website: https://github.com/secastel/phaser
      citation: >
        Rare variant phasing and haplotypic expression from RNA sequencing with phASER
        Stephane E. Castel1,2, Pejman Mohammadi1,2, Wendy K. Chung3, Yufeng Shen2,4 & Tuuli Lappalainen1,2
        Nature Communications volume 7, Article number: 12817 (2016)
    python_2_7_15:
      module: Python/2.7.15-GCCcore-8.2.0
      version: 2.7.15
      verbose: Python v2.7.15
      website: https://www.python.org
      citation: >
        Python Software Foundation. Python Language Reference, version 2.7.15. Available at http://www.python.org
    python_3_7_2:
      module: Python/3.7.2-foss-2019a
      version: 3.7.2
      verbose: Python v3.7.2
      website: https://www.python.org
      citation: >
        Python Software Foundation. Python Language Reference, version 3.7.2. Available at http://www.python.org
    R:
      module: R/3.6.1-phoenix
      version: "3.6.1"
      verbose: R v3.6.1
      website: https://www.r-project.org
      citation: >
        R Core Team (2017). R: A language and environment for statistical computing. R Foundation for
        Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
    rsem:
      module: RSEM/1.3.3
      version: "1.3.3"
      verbose: rsem v1.3.3
      website: https://github.com/deweylab/RSEM
      citation: >
        Li, B., Dewey, C.N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference
        genome. BMC Bioinformatics 12, 323 (2011). https://doi.org/10.1186/1471-2105-12-323
    salmon:
      module: Salmon/1.2.1-gompi-2019a
      version: "1.2.1"
      verbose: Salmon v1.2.1
      website: https://combine-lab.github.io/salmon/
      citation: >
        Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., & Kingsford, C. (2017). Salmon provides
        fast and bias-aware quantification of transcript expression. Nature Methods.
    sambamba:
      module: sambamba/0.7.0
      version: 0.7.0
      verbose: TODO
    samblaster:
      module: samblaster/0.1.24
      version: 0.1.24
      verbose: SaMBLAster TODO
    samtools:
      module: SAMtools/1.10-GCC-8.2.0-2.31.1
      version: "1.10"
      verbose: SAMtools v1.10
      website: http://www.htslib.org
      citation: >
        Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, and 1000
        Genome Project Data Processing Subgroup, The Sequence alignment/map (SAM) format and SAMtools,
        Bioinformatics (2009) 25(16) 2078-9 [19505943]
    sigprofiler:
      module: SigProfiler/1.1
      version: "1.1"
      verbose: SigProfiler v1.1
    singularity:
      module: singularity/3.5.2-phoenix
      version: "3.5.2"
      verbose: Singularity v3.5.2
      website: https://www.sylabs.io/singularity/
    snpeff:
      module: snpEff/4.3t-Java-1.8
      version: "4.3T"
      verbose: SnpEff v4.3T
      website: http://snpeff.sourceforge.net/index.html
      citation: >
        A program for annotating and predicting the effects of single
        nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila
        melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang
        le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin).
        2012 Apr-Jun;6(2):80-92. PMID: 22728672
    snpSniffer:
      module: snpSniffer/7.0.0-Java-11
      version: "7.0.0"
      verbose: snpSniffer v7.0.0
      website: https://github.com/tgen/snpSniffer
    star:
      module: STAR/2.7.5a
      version: 2.7.5a
      verbose: STAR v2.7.5a
      website: https://github.com/alexdobin/STAR
      citation: >
        Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P,
        Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner.
        Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub
        2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905.
    star_fusion:
      module: STAR-Fusion/1.8.1-GCC-8.2.0-2.31.1-Perl-5.28.1-Python-3.7.2
      version: 1.8.1
      verbose: STAR-Fusion v1.8.1
      website: https://github.com/STAR-Fusion/STAR-Fusion
      citation: >
        "STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq
        Brian Haas, Alexander Dobin, Nicolas Stransky, Bo Li, Xiao Yang, Timothy Tickle,
        Asma Bankapur, Carrie Ganote, Thomas Doak, Natalie Pochet, Jing Sun, Catherine Wu,
        Thomas Gingeras, Aviv Regev bioRxiv 120295; doi: https://doi.org/10.1101/120295"
    strelka:
      module: strelka/2.9.10-foss-2018b
      version: "2.9.10"
      verbose: Strelka2 Small Variant Caller v2.9.10
      website: https://github.com/Illumina/strelka
      citation: >
        Kim, S., Scheffler, K. et al. (2018) Strelka2: fast and accurate calling of germline and somatic
        variants. Nature Methods, 15, 591-594. doi:10.1038/s41592-018-0051-x
    subread:
      module: Subread/2.0.0-foss-2018b
      version: "2.0.0"
      verbose: Subread v2.0.0
      website: http://subread.sourceforge.net
      citation: >
        Liao Y, Smyth GK and Shi W. featureCounts: an efficient general-purpose program for assigning
        sequence reads to genomic features. Bioinformatics, 30(7):923-30, 2014
    tgen_mutation_burden:
      module: MutationBurden/1.2.3
      version: "1.2.3"
      verbose: TGen Mutation Burden Tool v1.2.3
    thred:
      module: tHReD/1.1.0
      version: "1.1.0"
      verbose: tHReD v1.1.0
    transparser:
      module: transParser/1.0.1
      version: "1.0.1"
      verbose: transParser v1.0.1
      website: https://github.com/tgen/transParser
    trinity:
      module: trinityrnaseq/2.8.6-gcc-8.2.0-2.31.1-perl-5.28.1
      version: "2.8.6"
      verbose: Trinity-v2.8.6
    vardict:
      module: vardict/1.7.0-java-1.8
      version: "1.7.0"
      verbose: Vardict Java v1.7.0
      website: https://github.com/AstraZeneca-NGS/VarDictJava
      citation: >
        Lai Z, Markovets A, Ahdesmaki M, Chapman B, Hofmann O, McEwen R, Johnson J, Dougherty B, Barrett
        JC, and Dry JR. VarDict: a novel and versatile variant caller for next-generation sequencing in
        cancer research. Nucleic Acids Res. 2016, pii: gkw227.
    vcfmerger2:
      module: vcfMerger2/0.8.7-phoenix
      version: "0.8.7"
      verbose: vcfMerger2 v0.8.7
      website: https://github.com/tgen/vcfMerger2
    vep:
      module: VEP/98.0-foss-2019a-Perl-5.28.1
      version: "98.3"
      verbose: ensembl-vep release 98.3
      website: https://github.com/Ensembl/ensembl-vep
      citation: >
        McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F.
        The Ensembl Variant Effect Predictor.
        Genome Biology Jun 6;17(1):122. (2016)
        doi:10.1186/s13059-016-0974-4
    verifybamid2:
      module: verifyBamID/1.0.6-foss-2019a
      version: 1.0.6
      website: https://github.com/Griffan/VerifyBamID
      citation: >
        Zhang F., Flickinger M., InPSYght Psychiatric Genetics Consortium, Abecasis G., Boehnke M.,
        Kang H.M.(8 November 2018)."Ancestry-agnostic estimation of DNA sample contamination from
        sequence reads".bioRxiv 466268; doi: https://doi.org/10.1101/466268
    vt:
      module: vt/0.57721-foss-2019a
      version: "0.57721"
      verbose: normalize v0.5
      website: https://genome.sph.umich.edu/wiki/Vt#Normalization
  phoenix:
    species: Homo sapiens
    genome_build: grch38_hg38
    genome_subversion_name: hg38tgen
    gene_model_name: ensembl_v98
    canonical_cds_intervals: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/Homo_sapiens.GRCh38.98.ucsc.cds_padded.final.bed
    capture_kit_path: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/tool_resources/capture_kits
    reference_fasta: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/genome_reference/GRCh38tgen_decoy_alts_hla.fa
    reference_fasta_2bit: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/genome_reference/GRCh38tgen_decoy_alts_hla.2bit
    reference_fai: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/genome_reference/GRCh38tgen_decoy_alts_hla.fa.fai
    reference_dict: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/genome_reference/GRCh38tgen_decoy_alts_hla.dict
    reference_non_N_interval_list: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/samtools_stats/GRCh38tgen_decoy_alts_hla_samstats_no_N_1based_primary_contigs_no_chrX_chrY.txt
    chip_fasta: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/bowtie2_2.3.5.1/GRCh38tgen_decoy_Ecoli.fa
    bowtie2_index_path: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/bowtie2_2.3.5.1
    bowtie2_index: GRCh38tgen_decoy
    bowtie2_chip_index: GRCh38tgen_decoy_Ecoli
    dbsnp: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/dbsnp/b154/dbSNP_b154_hg38tgen.bcf
    gnomad_exome: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/gnomad/r2.1.1/gnomad.exomes.r2.1.1.sites.liftover_grch38_AnnotationReference.bcf
    gnomad_genome: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/gnomad/r3.0/gnomad.genomes.r3.0.sites.pass.reduced.bcf
    gnomad_genome_per_chr: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/gnomad/r3.0/per_chromosome/gnomad.genomes.r3.0.sites.pass.reduced.
    gnomad_exome_mutect_germlinereference: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/gnomad/r2.1.1/gnomad.exomes.r2.1.1.sites.liftover_grch38_ForMutect.vcf.gz
    gnomad_genome_mutect_germlinereference: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/gnomad/r3.0/gnomad.genomes.r3.0.sites.pass.AnnotationReference.vcf.gz
    gnomad_exome_mutect_contamination: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/gnomad/r2.1.1/gnomad.exomes.r2.1.1.sites.liftover_grch38_ForMutectContamination.vcf.gz
    gnomad_genome_mutect_contamination: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/gnomad/r3.0/gnomad.genomes.r3.0.sites.pass.ForMutectContamination.vcf.gz
    cosmic_coding: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/cosmic/v92/CosmicCodingMuts_v92_hg38tgen.bcf
    cosmic_noncoding: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/cosmic/v92/CosmicNonCodingMuts_v92_hg38tgen.bcf
    clinvar: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/clinvar/20201020/clinvar_20201020_hg38tgen.bcf
    topmed: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/topmed/merged.BRAVO_TOPMed_Freeze_8.bcf
    bcftools_annotate_contig_update_ucsc2ensembl: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/bcftools/GRCh38_PrimaryContigs_UCSC_2_Ensembl_CrossMap.txt
    black_list: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/encode/Blacklist-2.0/lists/hg38-blacklist.v2.bed.gz
    chip_black_list: /home/tgenref/homo_sapiens/grch38_hg38/hs38dh/tool_specific_resources/ChIP_blacklist/hg38_blacklist.bed
    reference_msisensor_pro: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/msisensor_pro_v1.1.a/GRCh38tgen_decoy_alts_hla.microsatellites.list
    delly_annotation: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/tool_resources/delly/delly_anno_Homo_sapiens.GRCh38.98.ucsc.bed
    delly_exclusions: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/tool_resources/delly/hg38.excl
    delly_addRC_to_Delly_VCF_script: addRC_to_Delly_VCF_f4d178e.py
    delly_svtop_delly_sv_annotation_parellel_script: svtop.delly.sv_annotation.parallel_8820499.py
    manta_prepare_sv_vcf: manta_prepare_sv_vcf_f94bcc1.py
    manta_gene_annotation_parallel: manta_sv_annotation_parallel_8820499.py
    pairoscope_mm_igtx_calling_script: mm_igtx_pairoscope_calling_b38_356362b.py
    cna_seg_extend: seg_extend_229b8c7.py
    plotCNVplus_Rscript: plotCNVplus_4d89cb4.R
    plotSamStats_Rscript: summarize_samstats_8c45d63.R
    summarize_mm_igtx_Rscript: summarize_Ig_875a823.R
    process_assembled_bam: Process_Assembled_BAM_277eed7.py
    stats2json: samStats2json_3a90a2f.py
    stats2lims: uploadStats2Lims_1ace81f.py
    sigprofiler: sigprofiler_7595614.py
    annotSeg_script: annotSeg_7102f1c.pl
    cellranger_reference: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/tool_resources/cellranger_6.0.0/hg38tgen_ensembl_v98
    cellranger_vdj_reference: /home/tgenref/homo_sapiens/grch38_hg38/tool_specific_resources/cellranger/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0
    scrna_chemistry_options:
      X3SCR:
        chemistry_name: SC3Pv1
        umi_length: 10
        cell_barcode_whitelist_file: /packages/easy-build/software/CellRanger/6.0.0/lib/python/cellranger/barcodes/737K-april-2014_rc.txt
      XCSCR:
        chemistry_name: SC3Pv2
        umi_length: 10
        cell_barcode_whitelist_file: /packages/easy-build/software/CellRanger/6.0.0/lib/python/cellranger/barcodes/737K-august-2016.txt
      X3SC3:
        chemistry_name: SC3Pv3
        umi_length: 12
        cell_barcode_whitelist_file: /packages/easy-build/software/CellRanger/6.0.0/lib/python/cellranger/barcodes/3M-february-2018.txt
      X5SCR:
        chemistry_name: SC5P-R2
        umi_length: 10
        cell_barcode_whitelist_file: /packages/easy-build/software/CellRanger/6.0.0/lib/python/cellranger/barcodes/737K-august-2016.txt
      unknown:
        chemistry_name: auto
        umi_lenth: 10
        cell_barcode_whitelist_file: /packages/easy-build/software/CellRanger/6.0.0/lib/python/cellranger/barcodes/737K-august-2016.txt
    gatk_known_sites:
      - /home/tgenref/homo_sapiens/grch38_hg38/public_databases/broad_resource_bundle/Homo_sapiens_assembly38.dbsnp138.vcf
      - /home/tgenref/homo_sapiens/grch38_hg38/public_databases/broad_resource_bundle/Homo_sapiens_assembly38.known_indels.vcf.gz
      - /home/tgenref/homo_sapiens/grch38_hg38/public_databases/broad_resource_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
    gatk_cnn_resources:
      - /home/tgenref/homo_sapiens/grch38_hg38/public_databases/broad_resource_bundle/hapmap_3.3.hg38.vcf.gz
      - /home/tgenref/homo_sapiens/grch38_hg38/public_databases/broad_resource_bundle/Homo_sapiens_assembly38.known_indels.vcf.gz
      - /home/tgenref/homo_sapiens/grch38_hg38/public_databases/broad_resource_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
    mt_shifted_fa: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/gatk_mitochondrial/hg38_v0_chrM_Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta
    mt_shifted_chain: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/gatk_mitochondrial/hg38_v0_chrM_ShiftBack.chain
    mt_ref_fasta: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/gatk_mitochondrial/hg38_v0_chrM_Homo_sapiens_assembly38.chrM.fasta
    bwa_index: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/bwa_0.7.17/GRCh38tgen_decoy_alts_hla.fa
    bwa_mem2_index: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/bwa2_2.2.1/GRCh38tgen_decoy_alts_hla.fa
    gtf: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/Homo_sapiens.GRCh38.98.ucsc.gtf
    ref_flat: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/Homo_sapiens.GRCh38.98.ucsc.refFlat.txt
    ig_ENST_filter: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/disease_specific_resources/myeloma/Homo_sapiens_GRCh38_98_ucsc_ig_ENST_to_filter_out.tsv
    igtx_regions: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/disease_specific_resources/myeloma/Homo_sapiens_GRCh38_98_ucsc_igtx_regions.bed
    igtx_gene_regions: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/disease_specific_resources/myeloma/Homo_sapiens_GRCh38_98_ucsc_igtx_gene_regions.bed
    igtx_pairoscope_regions: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/disease_specific_resources/myeloma/Homo_sapiens_GRCh38_98_ucsc_igtx_pairoscope_regions.bed
    ribo_locations: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/Homo_sapiens.GRCh38.98.ucsc.ribo.interval_list
    gatk_cnv_primary_contigs_female: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/gatk_cnv/Homo_sapiens.GRCh38.primary.contigs.female.interval_list
    gatk_cnv_primary_contigs_male: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/gatk_cnv/Homo_sapiens.GRCh38.primary.contigs.male.interval_list
    encode_denylist: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/ncbi/Encode_deny_list_with_ncbi_centromere.merged.bed
    centromere: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/ncbi/Modeled_regions_for_GRCh38_centromere_blacklist_merged.bed
    mappability_track: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/bismap/k100.umap.no_header.bed
    rsem_index: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/tool_resources/rsem_1.3.3/hg38tgen
    transcriptome_fasta: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/Homo_sapiens.GRCh38.98.ucsc.transcriptome.fasta
    salmon_index: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/tool_resources/salmon_1.2.1-gompi-2019a/salmon_puff_75merPlus
    sex_check_targets: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/tgen_gender_check/chrx_common_dbSNPv152_snv_exons.bed
    sex_check_vcf: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/tgen_gender_check/chrx_common_dbSNPv152_snv_exons.vcf.gz
    star_fasta: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/genome_reference/GRCh38tgen_decoy.fa
    star_indices_path: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/tool_resources/star_2.7.5a
    starfusion_index: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/tool_resources/starFusion_gencode_v32/starFusion_Resources/ctat_genome_lib_build_dir
    strandedness_options:
      inward-unstranded-notapplicable:
        rsem: "none"
        salmon: "IU"
        htseq: "no"
        featurecounts: "0"
        tophat: "-fr-unstranded"
        collectrnaseqmetrics: "NONE"
      inward-stranded-forward:
        rsem: "forward"
        salmon: "ISF"
        htseq: "yes"
        featurecounts: "1"
        tophat: "-fr-secondstrand"
        collectrnaseqmetrics: "FIRST_READ_TRANSCRIPTION_STRAND"
      inward-stranded-reverse:
        rsem: "reverse"
        salmon: "ISR"
        htseq: "reverse"
        featurecounts: "2"
        tophat: "-fr-firststrand"
        collectrnaseqmetrics: "SECOND_READ_TRANSCRIPTION_STRAND"
    snpeff_config: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/tool_resources/snpEff_v4_3t/snpEff.config
    snpeff_data: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/tool_resources/snpEff_v4_3t/data
    snpeff_db: grch38.98
    snpeff_canonical_cds_intervals: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/Homo_sapiens.GRCh38.98.ucsc.cds_padded.snpeff_canonical.final.bed
    snpSniffer_sites: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/snpSniffer/positions_387_hg38_ucsc.txt
    snpSniffer_database: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/snpSniffer/databaseV5_hg38_ucsc.ini
    vep_data: /home/tgenref/homo_sapiens/grch38_hg38/tool_specific_resources/vep/v98/
    vep_canonical_cds_intervals: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/gene_model/ensembl_v98/Homo_sapiens.GRCh38.98.ucsc.cds_padded.vep_canonical.final.bed
    ns_effects:
      - 'splice_acceptor_variant'
      - 'splice_donor_variant'
      - 'start_lost'
      - 'exon_loss_variant'
      - 'frameshift_variant'
      - 'stop_gained'
      - 'stop_lost'
      - 'start_lost'
      - 'rare_amino_acid_variant'
      - 'missense_variant'
      - 'inframe_insertion'
      - 'disruptive_inframe_insertion'
      - 'inframe_deletion'
      - 'disruptive_inframe_deletion'
    deepvariant_models:
      exome: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/deepvariant_v0.10.0/DeepVariant-inception_v3-0.10.0+data-wes_standard/model.ckpt
      genome: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/deepvariant_v0.10.0/DeepVariant-inception_v3-0.10.0+data-wgs_standard/model.ckpt
    sequence_groupings:
      # Sequence groupings for BQSR (same groups as found in the GATK WDL example).
      - ['chr1']
      - ['chr2']
      - ['chr3']
      - ['chr4']
      - ['chr5']
      - ['chr6']
      - ['chr7']
      - ['chr8']
      - ['chr9']
      - ['chr10']
      - ['chr11']
      - ['chr12', 'chr13']
      - ['chr14', 'chr15']
      - ['chr16', 'chr17']
      - ['chr18', 'chr19', 'chr20']
      - ['chr21', 'chr22']
      - ['chrX', 'chrY', 'chrM', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270735v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270538v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270333v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000226v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chr1_KI270762v1_alt', 'chr1_KI270766v1_alt', 'chr1_KI270760v1_alt', 'chr1_KI270765v1_alt', 'chr1_GL383518v1_alt', 'chr1_GL383519v1_alt', 'chr1_GL383520v2_alt', 'chr1_KI270764v1_alt', 'chr1_KI270763v1_alt', 'chr1_KI270759v1_alt', 'chr1_KI270761v1_alt', 'chr2_KI270770v1_alt', 'chr2_KI270773v1_alt', 'chr2_KI270774v1_alt', 'chr2_KI270769v1_alt', 'chr2_GL383521v1_alt', 'chr2_KI270772v1_alt', 'chr2_KI270775v1_alt', 'chr2_KI270771v1_alt', 'chr2_KI270768v1_alt', 'chr2_GL582966v2_alt', 'chr2_GL383522v1_alt', 'chr2_KI270776v1_alt', 'chr2_KI270767v1_alt', 'chr3_JH636055v2_alt', 'chr3_KI270783v1_alt', 'chr3_KI270780v1_alt', 'chr3_GL383526v1_alt', 'chr3_KI270777v1_alt', 'chr3_KI270778v1_alt', 'chr3_KI270781v1_alt', 'chr3_KI270779v1_alt', 'chr3_KI270782v1_alt', 'chr3_KI270784v1_alt', 'chr4_KI270790v1_alt', 'chr4_GL383528v1_alt', 'chr4_KI270787v1_alt', 'chr4_GL000257v2_alt', 'chr4_KI270788v1_alt', 'chr4_GL383527v1_alt', 'chr4_KI270785v1_alt', 'chr4_KI270789v1_alt', 'chr4_KI270786v1_alt', 'chr5_KI270793v1_alt', 'chr5_KI270792v1_alt', 'chr5_KI270791v1_alt', 'chr5_GL383532v1_alt', 'chr5_GL949742v1_alt', 'chr5_KI270794v1_alt', 'chr5_GL339449v2_alt', 'chr5_GL383530v1_alt', 'chr5_KI270796v1_alt', 'chr5_GL383531v1_alt', 'chr5_KI270795v1_alt', 'chr6_GL000250v2_alt', 'chr6_KI270800v1_alt', 'chr6_KI270799v1_alt', 'chr6_GL383533v1_alt', 'chr6_KI270801v1_alt', 'chr6_KI270802v1_alt', 'chr6_KB021644v2_alt', 'chr6_KI270797v1_alt', 'chr6_KI270798v1_alt', 'chr7_KI270804v1_alt', 'chr7_KI270809v1_alt', 'chr7_KI270806v1_alt', 'chr7_GL383534v2_alt', 'chr7_KI270803v1_alt', 'chr7_KI270808v1_alt', 'chr7_KI270807v1_alt', 'chr7_KI270805v1_alt', 'chr8_KI270818v1_alt', 'chr8_KI270812v1_alt', 'chr8_KI270811v1_alt', 'chr8_KI270821v1_alt', 'chr8_KI270813v1_alt', 'chr8_KI270822v1_alt', 'chr8_KI270814v1_alt',]
      - ['chr8_KI270810v1_alt', 'chr8_KI270819v1_alt', 'chr8_KI270820v1_alt', 'chr8_KI270817v1_alt', 'chr8_KI270816v1_alt', 'chr8_KI270815v1_alt', 'chr9_GL383539v1_alt', 'chr9_GL383540v1_alt', 'chr9_GL383541v1_alt', 'chr9_GL383542v1_alt', 'chr9_KI270823v1_alt', 'chr10_GL383545v1_alt', 'chr10_KI270824v1_alt', 'chr10_GL383546v1_alt', 'chr10_KI270825v1_alt', 'chr11_KI270832v1_alt', 'chr11_KI270830v1_alt', 'chr11_KI270831v1_alt', 'chr11_KI270829v1_alt', 'chr11_GL383547v1_alt', 'chr11_JH159136v1_alt', 'chr11_JH159137v1_alt', 'chr11_KI270827v1_alt', 'chr11_KI270826v1_alt', 'chr12_GL877875v1_alt', 'chr12_GL877876v1_alt', 'chr12_KI270837v1_alt', 'chr12_GL383549v1_alt', 'chr12_KI270835v1_alt', 'chr12_GL383550v2_alt', 'chr12_GL383552v1_alt', 'chr12_GL383553v2_alt', 'chr12_KI270834v1_alt', 'chr12_GL383551v1_alt', 'chr12_KI270833v1_alt', 'chr12_KI270836v1_alt', 'chr13_KI270840v1_alt', 'chr13_KI270839v1_alt', 'chr13_KI270843v1_alt', 'chr13_KI270841v1_alt', 'chr13_KI270838v1_alt', 'chr13_KI270842v1_alt', 'chr14_KI270844v1_alt', 'chr14_KI270847v1_alt', 'chr14_KI270845v1_alt', 'chr14_KI270846v1_alt', 'chr15_KI270852v1_alt', 'chr15_KI270851v1_alt', 'chr15_KI270848v1_alt', 'chr15_GL383554v1_alt', 'chr15_KI270849v1_alt', 'chr15_GL383555v2_alt', 'chr15_KI270850v1_alt', 'chr16_KI270854v1_alt', 'chr16_KI270856v1_alt', 'chr16_KI270855v1_alt', 'chr16_KI270853v1_alt', 'chr16_GL383556v1_alt', 'chr16_GL383557v1_alt', 'chr17_GL383563v3_alt', 'chr17_KI270862v1_alt', 'chr17_KI270861v1_alt', 'chr17_KI270857v1_alt', 'chr17_JH159146v1_alt', 'chr17_JH159147v1_alt', 'chr17_GL383564v2_alt', 'chr17_GL000258v2_alt', 'chr17_GL383565v1_alt', 'chr17_KI270858v1_alt', 'chr17_KI270859v1_alt', 'chr17_GL383566v1_alt', 'chr17_KI270860v1_alt', 'chr18_KI270864v1_alt', 'chr18_GL383567v1_alt', 'chr18_GL383570v1_alt', 'chr18_GL383571v1_alt', 'chr18_GL383568v1_alt', 'chr18_GL383569v1_alt', 'chr18_GL383572v1_alt', 'chr18_KI270863v1_alt', 'chr19_KI270868v1_alt', 'chr19_KI270865v1_alt', 'chr19_GL383573v1_alt', 'chr19_GL383575v2_alt', 'chr19_GL383576v1_alt', 'chr19_GL383574v1_alt', 'chr19_KI270866v1_alt', 'chr19_KI270867v1_alt', 'chr19_GL949746v1_alt', 'chr20_GL383577v2_alt', 'chr20_KI270869v1_alt', 'chr20_KI270871v1_alt', 'chr20_KI270870v1_alt', 'chr21_GL383578v2_alt', 'chr21_KI270874v1_alt', 'chr21_KI270873v1_alt', 'chr21_GL383579v2_alt', 'chr21_GL383580v2_alt', 'chr21_GL383581v2_alt', 'chr21_KI270872v1_alt', 'chr22_KI270875v1_alt', 'chr22_KI270878v1_alt', 'chr22_KI270879v1_alt', 'chr22_KI270876v1_alt', 'chr22_KI270877v1_alt', 'chr22_GL383583v2_alt', 'chr22_GL383582v2_alt', 'chrX_KI270880v1_alt', 'chrX_KI270881v1_alt', 'chr19_KI270882v1_alt', 'chr19_KI270883v1_alt', 'chr19_KI270884v1_alt', 'chr19_KI270885v1_alt', 'chr19_KI270886v1_alt', 'chr19_KI270887v1_alt', 'chr19_KI270888v1_alt', 'chr19_KI270889v1_alt', 'chr19_KI270890v1_alt', 'chr19_KI270891v1_alt', 'chr1_KI270892v1_alt', 'chr2_KI270894v1_alt', 'chr2_KI270893v1_alt', 'chr3_KI270895v1_alt', 'chr4_KI270896v1_alt', 'chr5_KI270897v1_alt', 'chr5_KI270898v1_alt', 'chr6_GL000251v2_alt', 'chr7_KI270899v1_alt', 'chr8_KI270901v1_alt', 'chr8_KI270900v1_alt', 'chr11_KI270902v1_alt', 'chr11_KI270903v1_alt', 'chr12_KI270904v1_alt', 'chr15_KI270906v1_alt', 'chr15_KI270905v1_alt', 'chr17_KI270907v1_alt', 'chr17_KI270910v1_alt', 'chr17_KI270909v1_alt', 'chr17_JH159148v1_alt', 'chr17_KI270908v1_alt', 'chr18_KI270912v1_alt', 'chr18_KI270911v1_alt', 'chr19_GL949747v2_alt', 'chr22_KB663609v1_alt', 'chrX_KI270913v1_alt', 'chr19_KI270914v1_alt', 'chr19_KI270915v1_alt', 'chr19_KI270916v1_alt', 'chr19_KI270917v1_alt', 'chr19_KI270918v1_alt', 'chr19_KI270919v1_alt', 'chr19_KI270920v1_alt', 'chr19_KI270921v1_alt', 'chr19_KI270922v1_alt', 'chr19_KI270923v1_alt', 'chr3_KI270924v1_alt', 'chr4_KI270925v1_alt', 'chr6_GL000252v2_alt', 'chr8_KI270926v1_alt', 'chr11_KI270927v1_alt', 'chr19_GL949748v2_alt', 'chr22_KI270928v1_alt', 'chr19_KI270929v1_alt', 'chr19_KI270930v1_alt', 'chr19_KI270931v1_alt', 'chr19_KI270932v1_alt', 'chr19_KI270933v1_alt', 'chr19_GL000209v2_alt', 'chr3_KI270934v1_alt', 'chr6_GL000253v2_alt', 'chr19_GL949749v2_alt', 'chr3_KI270935v1_alt', 'chr6_GL000254v2_alt', 'chr19_GL949750v2_alt', 'chr3_KI270936v1_alt', 'chr6_GL000255v2_alt', 'chr19_GL949751v2_alt', 'chr3_KI270937v1_alt', 'chr6_GL000256v2_alt', 'chr19_GL949752v1_alt', 'chr6_KI270758v1_alt', 'chr19_GL949753v2_alt', 'chr19_KI270938v1_alt', 'chrEBV', 'chrUn_KN707606v1_decoy', 'chrUn_KN707607v1_decoy', 'chrUn_KN707608v1_decoy', 'chrUn_KN707609v1_decoy', 'chrUn_KN707610v1_decoy', 'chrUn_KN707611v1_decoy', 'chrUn_KN707612v1_decoy', 'chrUn_KN707613v1_decoy', 'chrUn_KN707614v1_decoy', 'chrUn_KN707615v1_decoy', 'chrUn_KN707616v1_decoy', 'chrUn_KN707617v1_decoy', 'chrUn_KN707618v1_decoy', 'chrUn_KN707619v1_decoy', 'chrUn_KN707620v1_decoy', 'chrUn_KN707621v1_decoy', 'chrUn_KN707622v1_decoy', 'chrUn_KN707623v1_decoy', 'chrUn_KN707624v1_decoy', 'chrUn_KN707625v1_decoy', 'chrUn_KN707626v1_decoy', 'chrUn_KN707627v1_decoy', 'chrUn_KN707628v1_decoy', 'chrUn_KN707629v1_decoy', 'chrUn_KN707630v1_decoy', 'chrUn_KN707631v1_decoy', 'chrUn_KN707632v1_decoy', 'chrUn_KN707633v1_decoy', 'chrUn_KN707634v1_decoy', 'chrUn_KN707635v1_decoy', 'chrUn_KN707636v1_decoy', 'chrUn_KN707637v1_decoy', 'chrUn_KN707638v1_decoy', 'chrUn_KN707639v1_decoy', 'chrUn_KN707640v1_decoy', 'chrUn_KN707641v1_decoy', 'chrUn_KN707642v1_decoy', 'chrUn_KN707643v1_decoy', 'chrUn_KN707644v1_decoy', 'chrUn_KN707645v1_decoy', 'chrUn_KN707646v1_decoy', 'chrUn_KN707647v1_decoy', 'chrUn_KN707648v1_decoy', 'chrUn_KN707649v1_decoy', 'chrUn_KN707650v1_decoy', 'chrUn_KN707651v1_decoy', 'chrUn_KN707652v1_decoy', 'chrUn_KN707653v1_decoy', 'chrUn_KN707654v1_decoy', 'chrUn_KN707655v1_decoy', 'chrUn_KN707656v1_decoy', 'chrUn_KN707657v1_decoy', 'chrUn_KN707658v1_decoy', 'chrUn_KN707659v1_decoy', 'chrUn_KN707660v1_decoy', 'chrUn_KN707661v1_decoy', 'chrUn_KN707662v1_decoy', 'chrUn_KN707663v1_decoy', 'chrUn_KN707664v1_decoy', 'chrUn_KN707665v1_decoy', 'chrUn_KN707666v1_decoy', 'chrUn_KN707667v1_decoy', 'chrUn_KN707668v1_decoy', 'chrUn_KN707669v1_decoy', 'chrUn_KN707670v1_decoy', 'chrUn_KN707671v1_decoy', 'chrUn_KN707672v1_decoy', 'chrUn_KN707673v1_decoy', 'chrUn_KN707674v1_decoy', 'chrUn_KN707675v1_decoy', 'chrUn_KN707676v1_decoy', 'chrUn_KN707677v1_decoy', 'chrUn_KN707678v1_decoy', 'chrUn_KN707679v1_decoy', 'chrUn_KN707680v1_decoy', 'chrUn_KN707681v1_decoy', 'chrUn_KN707682v1_decoy', 'chrUn_KN707683v1_decoy', 'chrUn_KN707684v1_decoy', 'chrUn_KN707685v1_decoy', 'chrUn_KN707686v1_decoy', 'chrUn_KN707687v1_decoy', 'chrUn_KN707688v1_decoy', 'chrUn_KN707689v1_decoy', 'chrUn_KN707690v1_decoy', 'chrUn_KN707691v1_decoy', 'chrUn_KN707692v1_decoy', 'chrUn_KN707693v1_decoy', 'chrUn_KN707694v1_decoy', 'chrUn_KN707695v1_decoy', 'chrUn_KN707696v1_decoy', 'chrUn_KN707697v1_decoy', 'chrUn_KN707698v1_decoy', 'chrUn_KN707699v1_decoy', 'chrUn_KN707700v1_decoy', 'chrUn_KN707701v1_decoy', 'chrUn_KN707702v1_decoy', 'chrUn_KN707703v1_decoy', 'chrUn_KN707704v1_decoy', 'chrUn_KN707705v1_decoy', 'chrUn_KN707706v1_decoy', 'chrUn_KN707707v1_decoy', 'chrUn_KN707708v1_decoy', 'chrUn_KN707709v1_decoy', 'chrUn_KN707710v1_decoy', 'chrUn_KN707711v1_decoy', 'chrUn_KN707712v1_decoy', 'chrUn_KN707713v1_decoy', 'chrUn_KN707714v1_decoy', 'chrUn_KN707715v1_decoy', 'chrUn_KN707716v1_decoy', 'chrUn_KN707717v1_decoy', 'chrUn_KN707718v1_decoy', 'chrUn_KN707719v1_decoy', 'chrUn_KN707720v1_decoy', 'chrUn_KN707721v1_decoy', 'chrUn_KN707722v1_decoy', 'chrUn_KN707723v1_decoy', 'chrUn_KN707724v1_decoy', 'chrUn_KN707725v1_decoy', 'chrUn_KN707726v1_decoy', 'chrUn_KN707727v1_decoy', 'chrUn_KN707728v1_decoy', 'chrUn_KN707729v1_decoy', 'chrUn_KN707730v1_decoy', 'chrUn_KN707731v1_decoy', 'chrUn_KN707732v1_decoy', 'chrUn_KN707733v1_decoy', 'chrUn_KN707734v1_decoy', 'chrUn_KN707735v1_decoy', 'chrUn_KN707736v1_decoy', 'chrUn_KN707737v1_decoy', 'chrUn_KN707738v1_decoy', 'chrUn_KN707739v1_decoy', 'chrUn_KN707740v1_decoy', 'chrUn_KN707741v1_decoy', 'chrUn_KN707742v1_decoy', 'chrUn_KN707743v1_decoy', 'chrUn_KN707744v1_decoy', 'chrUn_KN707745v1_decoy', 'chrUn_KN707746v1_decoy', 'chrUn_KN707747v1_decoy', 'chrUn_KN707748v1_decoy', 'chrUn_KN707749v1_decoy', 'chrUn_KN707750v1_decoy', 'chrUn_KN707751v1_decoy', 'chrUn_KN707752v1_decoy', 'chrUn_KN707753v1_decoy', 'chrUn_KN707754v1_decoy', 'chrUn_KN707755v1_decoy', 'chrUn_KN707756v1_decoy', 'chrUn_KN707757v1_decoy', 'chrUn_KN707758v1_decoy', 'chrUn_KN707759v1_decoy', 'chrUn_KN707760v1_decoy', 'chrUn_KN707761v1_decoy', 'chrUn_KN707762v1_decoy', 'chrUn_KN707763v1_decoy', 'chrUn_KN707764v1_decoy', 'chrUn_KN707765v1_decoy', 'chrUn_KN707766v1_decoy', 'chrUn_KN707767v1_decoy', 'chrUn_KN707768v1_decoy', 'chrUn_KN707769v1_decoy', 'chrUn_KN707770v1_decoy', 'chrUn_KN707771v1_decoy', 'chrUn_KN707772v1_decoy', 'chrUn_KN707773v1_decoy', 'chrUn_KN707774v1_decoy', 'chrUn_KN707775v1_decoy', 'chrUn_KN707776v1_decoy', 'chrUn_KN707777v1_decoy', 'chrUn_KN707778v1_decoy', 'chrUn_KN707779v1_decoy', 'chrUn_KN707780v1_decoy', 'chrUn_KN707781v1_decoy', 'chrUn_KN707782v1_decoy', 'chrUn_KN707783v1_decoy', 'chrUn_KN707784v1_decoy', 'chrUn_KN707785v1_decoy', 'chrUn_KN707786v1_decoy', 'chrUn_KN707787v1_decoy', 'chrUn_KN707788v1_decoy', 'chrUn_KN707789v1_decoy', 'chrUn_KN707790v1_decoy', 'chrUn_KN707791v1_decoy', 'chrUn_KN707792v1_decoy', 'chrUn_KN707793v1_decoy', 'chrUn_KN707794v1_decoy', 'chrUn_KN707795v1_decoy', 'chrUn_KN707796v1_decoy', 'chrUn_KN707797v1_decoy', 'chrUn_KN707798v1_decoy', 'chrUn_KN707799v1_decoy', 'chrUn_KN707800v1_decoy', 'chrUn_KN707801v1_decoy', 'chrUn_KN707802v1_decoy', 'chrUn_KN707803v1_decoy', 'chrUn_KN707804v1_decoy', 'chrUn_KN707805v1_decoy', 'chrUn_KN707806v1_decoy', 'chrUn_KN707807v1_decoy', 'chrUn_KN707808v1_decoy', 'chrUn_KN707809v1_decoy', 'chrUn_KN707810v1_decoy', 'chrUn_KN707811v1_decoy', 'chrUn_KN707812v1_decoy', 'chrUn_KN707813v1_decoy', 'chrUn_KN707814v1_decoy', 'chrUn_KN707815v1_decoy', 'chrUn_KN707816v1_decoy', 'chrUn_KN707817v1_decoy', 'chrUn_KN707818v1_decoy', 'chrUn_KN707819v1_decoy', 'chrUn_KN707820v1_decoy', 'chrUn_KN707821v1_decoy', 'chrUn_KN707822v1_decoy', 'chrUn_KN707823v1_decoy', 'chrUn_KN707824v1_decoy', 'chrUn_KN707825v1_decoy', 'chrUn_KN707826v1_decoy', 'chrUn_KN707827v1_decoy', 'chrUn_KN707828v1_decoy', 'chrUn_KN707829v1_decoy', 'chrUn_KN707830v1_decoy', 'chrUn_KN707831v1_decoy', 'chrUn_KN707832v1_decoy', 'chrUn_KN707833v1_decoy', 'chrUn_KN707834v1_decoy', 'chrUn_KN707835v1_decoy', 'chrUn_KN707836v1_decoy', 'chrUn_KN707837v1_decoy', 'chrUn_KN707838v1_decoy', 'chrUn_KN707839v1_decoy', 'chrUn_KN707840v1_decoy', 'chrUn_KN707841v1_decoy', 'chrUn_KN707842v1_decoy', 'chrUn_KN707843v1_decoy', 'chrUn_KN707844v1_decoy', 'chrUn_KN707845v1_decoy', 'chrUn_KN707846v1_decoy', 'chrUn_KN707847v1_decoy', 'chrUn_KN707848v1_decoy', 'chrUn_KN707849v1_decoy', 'chrUn_KN707850v1_decoy', 'chrUn_KN707851v1_decoy', 'chrUn_KN707852v1_decoy', 'chrUn_KN707853v1_decoy', 'chrUn_KN707854v1_decoy', 'chrUn_KN707855v1_decoy', 'chrUn_KN707856v1_decoy', 'chrUn_KN707857v1_decoy', 'chrUn_KN707858v1_decoy', 'chrUn_KN707859v1_decoy', 'chrUn_KN707860v1_decoy', 'chrUn_KN707861v1_decoy', 'chrUn_KN707862v1_decoy', 'chrUn_KN707863v1_decoy', 'chrUn_KN707864v1_decoy', 'chrUn_KN707865v1_decoy', 'chrUn_KN707866v1_decoy', 'chrUn_KN707867v1_decoy', 'chrUn_KN707868v1_decoy', 'chrUn_KN707869v1_decoy', 'chrUn_KN707870v1_decoy', 'chrUn_KN707871v1_decoy', 'chrUn_KN707872v1_decoy', 'chrUn_KN707873v1_decoy', 'chrUn_KN707874v1_decoy', 'chrUn_KN707875v1_decoy', 'chrUn_KN707876v1_decoy', 'chrUn_KN707877v1_decoy', 'chrUn_KN707878v1_decoy', 'chrUn_KN707879v1_decoy', 'chrUn_KN707880v1_decoy', 'chrUn_KN707881v1_decoy', 'chrUn_KN707882v1_decoy', 'chrUn_KN707883v1_decoy', 'chrUn_KN707884v1_decoy', 'chrUn_KN707885v1_decoy', 'chrUn_KN707886v1_decoy', 'chrUn_KN707887v1_decoy', 'chrUn_KN707888v1_decoy', 'chrUn_KN707889v1_decoy', 'chrUn_KN707890v1_decoy', 'chrUn_KN707891v1_decoy', 'chrUn_KN707892v1_decoy', 'chrUn_KN707893v1_decoy', 'chrUn_KN707894v1_decoy', 'chrUn_KN707895v1_decoy', 'chrUn_KN707896v1_decoy', 'chrUn_KN707897v1_decoy', 'chrUn_KN707898v1_decoy', 'chrUn_KN707899v1_decoy', 'chrUn_KN707900v1_decoy', 'chrUn_KN707901v1_decoy', 'chrUn_KN707902v1_decoy', 'chrUn_KN707903v1_decoy', 'chrUn_KN707904v1_decoy', 'chrUn_KN707905v1_decoy', 'chrUn_KN707906v1_decoy', 'chrUn_KN707907v1_decoy', 'chrUn_KN707908v1_decoy', 'chrUn_KN707909v1_decoy', 'chrUn_KN707910v1_decoy', 'chrUn_KN707911v1_decoy', 'chrUn_KN707912v1_decoy', 'chrUn_KN707913v1_decoy', 'chrUn_KN707914v1_decoy', 'chrUn_KN707915v1_decoy', 'chrUn_KN707916v1_decoy', 'chrUn_KN707917v1_decoy', 'chrUn_KN707918v1_decoy', 'chrUn_KN707919v1_decoy', 'chrUn_KN707920v1_decoy', 'chrUn_KN707921v1_decoy', 'chrUn_KN707922v1_decoy', 'chrUn_KN707923v1_decoy', 'chrUn_KN707924v1_decoy', 'chrUn_KN707925v1_decoy', 'chrUn_KN707926v1_decoy', 'chrUn_KN707927v1_decoy', 'chrUn_KN707928v1_decoy', 'chrUn_KN707929v1_decoy', 'chrUn_KN707930v1_decoy', 'chrUn_KN707931v1_decoy', 'chrUn_KN707932v1_decoy', 'chrUn_KN707933v1_decoy', 'chrUn_KN707934v1_decoy', 'chrUn_KN707935v1_decoy', 'chrUn_KN707936v1_decoy', 'chrUn_KN707937v1_decoy', 'chrUn_KN707938v1_decoy', 'chrUn_KN707939v1_decoy', 'chrUn_KN707940v1_decoy', 'chrUn_KN707941v1_decoy', 'chrUn_KN707942v1_decoy', 'chrUn_KN707943v1_decoy', 'chrUn_KN707944v1_decoy', 'chrUn_KN707945v1_decoy', 'chrUn_KN707946v1_decoy', 'chrUn_KN707947v1_decoy', 'chrUn_KN707948v1_decoy', 'chrUn_KN707949v1_decoy', 'chrUn_KN707950v1_decoy', 'chrUn_KN707951v1_decoy', 'chrUn_KN707952v1_decoy', 'chrUn_KN707953v1_decoy', 'chrUn_KN707954v1_decoy', 'chrUn_KN707955v1_decoy', 'chrUn_KN707956v1_decoy', 'chrUn_KN707957v1_decoy', 'chrUn_KN707958v1_decoy', 'chrUn_KN707959v1_decoy', 'chrUn_KN707960v1_decoy', 'chrUn_KN707961v1_decoy', 'chrUn_KN707962v1_decoy', 'chrUn_KN707963v1_decoy', 'chrUn_KN707964v1_decoy', 'chrUn_KN707965v1_decoy', 'chrUn_KN707966v1_decoy', 'chrUn_KN707967v1_decoy', 'chrUn_KN707968v1_decoy', 'chrUn_KN707969v1_decoy', 'chrUn_KN707970v1_decoy', 'chrUn_KN707971v1_decoy', 'chrUn_KN707972v1_decoy', 'chrUn_KN707973v1_decoy', 'chrUn_KN707974v1_decoy', 'chrUn_KN707975v1_decoy', 'chrUn_KN707976v1_decoy', 'chrUn_KN707977v1_decoy', 'chrUn_KN707978v1_decoy', 'chrUn_KN707979v1_decoy', 'chrUn_KN707980v1_decoy', 'chrUn_KN707981v1_decoy', 'chrUn_KN707982v1_decoy', 'chrUn_KN707983v1_decoy', 'chrUn_KN707984v1_decoy', 'chrUn_KN707985v1_decoy', 'chrUn_KN707986v1_decoy', 'chrUn_KN707987v1_decoy', 'chrUn_KN707988v1_decoy', 'chrUn_KN707989v1_decoy', 'chrUn_KN707990v1_decoy', 'chrUn_KN707991v1_decoy', 'chrUn_KN707992v1_decoy', 'chrUn_JTFH01000001v1_decoy', 'chrUn_JTFH01000002v1_decoy', 'chrUn_JTFH01000003v1_decoy', 'chrUn_JTFH01000004v1_decoy', 'chrUn_JTFH01000005v1_decoy', 'chrUn_JTFH01000006v1_decoy', 'chrUn_JTFH01000007v1_decoy', 'chrUn_JTFH01000008v1_decoy', 'chrUn_JTFH01000009v1_decoy', 'chrUn_JTFH01000010v1_decoy', 'chrUn_JTFH01000011v1_decoy', 'chrUn_JTFH01000012v1_decoy', 'chrUn_JTFH01000013v1_decoy', 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'HLA-A*33:07', 'HLA-A*34:01:01', 'HLA-A*34:02:01', 'HLA-A*36:01', 'HLA-A*43:01', 'HLA-A*66:01:01', 'HLA-A*66:17', 'HLA-A*68:01:01:01', 'HLA-A*68:01:01:02', 'HLA-A*68:01:02:01', 'HLA-A*68:01:02:02', 'HLA-A*68:02:01:01', 'HLA-A*68:02:01:02', 'HLA-A*68:02:01:03', 'HLA-A*68:02:02', 'HLA-A*68:03:01', 'HLA-A*68:08:01', 'HLA-A*68:113', 'HLA-A*68:17', 'HLA-A*68:18N', 'HLA-A*68:22', 'HLA-A*68:71', 'HLA-A*69:01', 'HLA-A*74:01', 'HLA-A*74:02:01:01', 'HLA-A*74:02:01:02', 'HLA-A*80:01:01:01', 'HLA-A*80:01:01:02', 'HLA-B*07:02:01', 'HLA-B*07:05:01', 'HLA-B*07:06', 'HLA-B*07:156', 'HLA-B*07:33:01', 'HLA-B*07:41', 'HLA-B*07:44', 'HLA-B*07:50', 'HLA-B*08:01:01', 'HLA-B*08:08N', 'HLA-B*08:132', 'HLA-B*08:134', 'HLA-B*08:19N', 'HLA-B*08:20', 'HLA-B*08:33', 'HLA-B*08:79', 'HLA-B*13:01:01', 'HLA-B*13:02:01', 'HLA-B*13:02:03', 'HLA-B*13:02:09', 'HLA-B*13:08', 'HLA-B*13:15', 'HLA-B*13:25', 'HLA-B*14:01:01', 'HLA-B*14:02:01', 'HLA-B*14:07N', 'HLA-B*15:01:01:01', 'HLA-B*15:01:01:02N', 'HLA-B*15:01:01:03', 'HLA-B*15:02:01', 'HLA-B*15:03:01', 'HLA-B*15:04:01', 'HLA-B*15:07:01', 'HLA-B*15:108', 'HLA-B*15:10:01', 'HLA-B*15:11:01', 'HLA-B*15:13:01', 'HLA-B*15:16:01', 'HLA-B*15:17:01:01', 'HLA-B*15:17:01:02', 'HLA-B*15:18:01', 'HLA-B*15:220', 'HLA-B*15:25:01', 'HLA-B*15:27:01', 'HLA-B*15:32:01', 'HLA-B*15:42', 'HLA-B*15:58', 'HLA-B*15:66', 'HLA-B*15:77', 'HLA-B*15:83', 'HLA-B*18:01:01:01', 'HLA-B*18:01:01:02', 'HLA-B*18:02', 'HLA-B*18:03', 'HLA-B*18:17N', 'HLA-B*18:26', 'HLA-B*18:94N', 'HLA-B*27:04:01', 'HLA-B*27:05:02', 'HLA-B*27:05:18', 'HLA-B*27:06', 'HLA-B*27:07:01', 'HLA-B*27:131', 'HLA-B*27:24', 'HLA-B*27:25', 'HLA-B*27:32', 'HLA-B*35:01:01:01', 'HLA-B*35:01:01:02', 'HLA-B*35:01:22', 'HLA-B*35:02:01', 'HLA-B*35:03:01', 'HLA-B*35:05:01', 'HLA-B*35:08:01', 'HLA-B*35:14:02', 'HLA-B*35:241', 'HLA-B*35:41', 'HLA-B*37:01:01', 'HLA-B*37:01:05', 'HLA-B*38:01:01', 'HLA-B*38:02:01', 'HLA-B*38:14', 'HLA-B*39:01:01:01', 'HLA-B*39:01:01:02L', 'HLA-B*39:01:01:03', 'HLA-B*39:01:03', 'HLA-B*39:01:16', 'HLA-B*39:01:21', 'HLA-B*39:05:01', 'HLA-B*39:06:02', 'HLA-B*39:10:01', 'HLA-B*39:13:02', 'HLA-B*39:14', 'HLA-B*39:34', 'HLA-B*39:38Q', 'HLA-B*40:01:01', 'HLA-B*40:01:02', 'HLA-B*40:02:01', 'HLA-B*40:03', 'HLA-B*40:06:01:01', 'HLA-B*40:06:01:02', 'HLA-B*40:10:01', 'HLA-B*40:150', 'HLA-B*40:40', 'HLA-B*40:72:01', 'HLA-B*40:79', 'HLA-B*41:01:01', 'HLA-B*41:02:01', 'HLA-B*42:01:01', 'HLA-B*42:02', 'HLA-B*42:08', 'HLA-B*44:02:01:01', 'HLA-B*44:02:01:02S', 'HLA-B*44:02:01:03', 'HLA-B*44:02:17', 'HLA-B*44:02:27', 'HLA-B*44:03:01', 'HLA-B*44:03:02', 'HLA-B*44:04', 'HLA-B*44:09', 'HLA-B*44:138Q', 'HLA-B*44:150', 'HLA-B*44:23N', 'HLA-B*44:26', 'HLA-B*44:46', 'HLA-B*44:49', 'HLA-B*44:56N', 'HLA-B*45:01:01', 'HLA-B*45:04', 'HLA-B*46:01:01', 'HLA-B*46:01:05', 'HLA-B*47:01:01:01', 'HLA-B*47:01:01:02', 'HLA-B*48:01:01', 'HLA-B*48:03:01', 'HLA-B*48:04', 'HLA-B*48:08', 'HLA-B*49:01:01', 'HLA-B*49:32', 'HLA-B*50:01:01', 'HLA-B*51:01:01', 'HLA-B*51:01:02', 'HLA-B*51:02:01', 'HLA-B*51:07:01', 'HLA-B*51:42', 'HLA-B*52:01:01:01', 'HLA-B*52:01:01:02', 'HLA-B*52:01:01:03', 'HLA-B*52:01:02', 'HLA-B*53:01:01', 'HLA-B*53:11', 'HLA-B*54:01:01', 'HLA-B*54:18', 'HLA-B*55:01:01', 'HLA-B*55:01:03', 'HLA-B*55:02:01', 'HLA-B*55:12', 'HLA-B*55:24', 'HLA-B*55:48', 'HLA-B*56:01:01', 'HLA-B*56:03', 'HLA-B*56:04', 'HLA-B*57:01:01', 'HLA-B*57:03:01', 'HLA-B*57:06', 'HLA-B*57:11', 'HLA-B*57:29', 'HLA-B*58:01:01', 'HLA-B*58:31N', 'HLA-B*59:01:01:01', 'HLA-B*59:01:01:02', 'HLA-B*67:01:01', 'HLA-B*67:01:02', 'HLA-B*67:02', 'HLA-B*73:01', 'HLA-B*78:01:01', 'HLA-B*81:01', 'HLA-B*82:02:01', 'HLA-C*01:02:01', 'HLA-C*01:02:11', 'HLA-C*01:02:29', 'HLA-C*01:02:30', 'HLA-C*01:03', 'HLA-C*01:06', 'HLA-C*01:08', 'HLA-C*01:14', 'HLA-C*01:21', 'HLA-C*01:30', 'HLA-C*01:40', 'HLA-C*02:02:02:01', 'HLA-C*02:02:02:02', 'HLA-C*02:10', 'HLA-C*02:11', 'HLA-C*02:16:02', 'HLA-C*02:69', 'HLA-C*02:85', 'HLA-C*02:86', 'HLA-C*02:87', 'HLA-C*03:02:01', 'HLA-C*03:02:02:01', 'HLA-C*03:02:02:02', 'HLA-C*03:02:02:03', 'HLA-C*03:03:01', 'HLA-C*03:04:01:01', 'HLA-C*03:04:01:02', 'HLA-C*03:04:02', 'HLA-C*03:04:04', 'HLA-C*03:05', 'HLA-C*03:06', 'HLA-C*03:100', 'HLA-C*03:13:01', 'HLA-C*03:20N', 'HLA-C*03:219', 'HLA-C*03:261', 'HLA-C*03:40:01', 'HLA-C*03:41:02', 'HLA-C*03:46', 'HLA-C*03:61', 'HLA-C*04:01:01:01', 'HLA-C*04:01:01:02', 'HLA-C*04:01:01:03', 'HLA-C*04:01:01:04', 'HLA-C*04:01:01:05', 'HLA-C*04:01:62', 'HLA-C*04:03:01', 'HLA-C*04:06', 'HLA-C*04:09N', 'HLA-C*04:128', 'HLA-C*04:161', 'HLA-C*04:177', 'HLA-C*04:70', 'HLA-C*04:71', 'HLA-C*05:01:01:01', 'HLA-C*05:01:01:02', 'HLA-C*05:08', 'HLA-C*05:09:01', 'HLA-C*05:93', 'HLA-C*06:02:01:01', 'HLA-C*06:02:01:02', 'HLA-C*06:02:01:03', 'HLA-C*06:23', 'HLA-C*06:24', 'HLA-C*06:46N', 'HLA-C*07:01:01:01', 'HLA-C*07:01:01:02', 'HLA-C*07:01:02', 'HLA-C*07:01:19', 'HLA-C*07:01:27', 'HLA-C*07:01:45', 'HLA-C*07:02:01:01', 'HLA-C*07:02:01:02', 'HLA-C*07:02:01:03', 'HLA-C*07:02:01:04', 'HLA-C*07:02:01:05', 'HLA-C*07:02:05', 'HLA-C*07:02:06', 'HLA-C*07:02:64', 'HLA-C*07:04:01', 'HLA-C*07:04:02', 'HLA-C*07:06', 'HLA-C*07:149', 'HLA-C*07:18', 'HLA-C*07:19', 'HLA-C*07:26', 'HLA-C*07:30', 'HLA-C*07:32N', 'HLA-C*07:384', 'HLA-C*07:385', 'HLA-C*07:386', 'HLA-C*07:391', 'HLA-C*07:392', 'HLA-C*07:49', 'HLA-C*07:56:02', 'HLA-C*07:66', 'HLA-C*07:67', 'HLA-C*08:01:01', 'HLA-C*08:01:03', 'HLA-C*08:02:01:01', 'HLA-C*08:02:01:02', 'HLA-C*08:03:01', 'HLA-C*08:04:01', 'HLA-C*08:112', 'HLA-C*08:20', 'HLA-C*08:21', 'HLA-C*08:22', 'HLA-C*08:24', 'HLA-C*08:27', 'HLA-C*08:36N', 'HLA-C*08:40', 'HLA-C*08:41', 'HLA-C*08:62', 'HLA-C*12:02:02', 'HLA-C*12:03:01:01', 'HLA-C*12:03:01:02', 'HLA-C*12:08', 'HLA-C*12:13', 'HLA-C*12:19', 'HLA-C*12:22', 'HLA-C*12:99', 'HLA-C*14:02:01', 'HLA-C*14:03', 'HLA-C*14:21N', 'HLA-C*14:23', 'HLA-C*15:02:01', 'HLA-C*15:05:01', 'HLA-C*15:05:02', 'HLA-C*15:13', 'HLA-C*15:16', 'HLA-C*15:17', 'HLA-C*15:96Q', 'HLA-C*16:01:01', 'HLA-C*16:02:01', 'HLA-C*16:04:01', 'HLA-C*17:01:01:01', 'HLA-C*17:01:01:02', 'HLA-C*17:01:01:03', 'HLA-C*17:03', 'HLA-C*18:01', 'HLA-DQA1*01:01:02', 'HLA-DQA1*01:02:01:01', 'HLA-DQA1*01:02:01:02', 'HLA-DQA1*01:02:01:03', 'HLA-DQA1*01:02:01:04', 'HLA-DQA1*01:03:01:01', 'HLA-DQA1*01:03:01:02', 'HLA-DQA1*01:04:01:01', 'HLA-DQA1*01:04:01:02', 'HLA-DQA1*01:05:01', 'HLA-DQA1*01:07', 'HLA-DQA1*01:10', 'HLA-DQA1*01:11', 'HLA-DQA1*02:01', 'HLA-DQA1*03:01:01', 'HLA-DQA1*03:02', 'HLA-DQA1*03:03:01', 'HLA-DQA1*04:01:02:01', 'HLA-DQA1*04:01:02:02', 'HLA-DQA1*04:02', 'HLA-DQA1*05:01:01:01', 'HLA-DQA1*05:01:01:02', 'HLA-DQA1*05:03', 'HLA-DQA1*05:05:01:01', 'HLA-DQA1*05:05:01:02', 'HLA-DQA1*05:05:01:03', 'HLA-DQA1*05:11', 'HLA-DQA1*06:01:01', 'HLA-DQB1*02:01:01', 'HLA-DQB1*02:02:01', 'HLA-DQB1*03:01:01:01', 'HLA-DQB1*03:01:01:02', 'HLA-DQB1*03:01:01:03', 'HLA-DQB1*03:02:01', 'HLA-DQB1*03:03:02:01', 'HLA-DQB1*03:03:02:02', 'HLA-DQB1*03:03:02:03', 'HLA-DQB1*03:05:01', 'HLA-DQB1*05:01:01:01', 'HLA-DQB1*05:01:01:02', 'HLA-DQB1*05:03:01:01', 'HLA-DQB1*05:03:01:02', 'HLA-DQB1*06:01:01', 'HLA-DQB1*06:02:01', 'HLA-DQB1*06:03:01', 'HLA-DQB1*06:09:01', 'HLA-DRB1*01:01:01', 'HLA-DRB1*01:02:01', 'HLA-DRB1*03:01:01:01', 'HLA-DRB1*03:01:01:02', 'HLA-DRB1*04:03:01', 'HLA-DRB1*07:01:01:01', 'HLA-DRB1*07:01:01:02', 'HLA-DRB1*08:03:02', 'HLA-DRB1*09:21', 'HLA-DRB1*10:01:01', 'HLA-DRB1*11:01:01', 'HLA-DRB1*11:01:02', 'HLA-DRB1*11:04:01', 'HLA-DRB1*12:01:01', 'HLA-DRB1*12:17', 'HLA-DRB1*13:01:01', 'HLA-DRB1*13:02:01', 'HLA-DRB1*14:05:01', 'HLA-DRB1*14:54:01', 'HLA-DRB1*15:01:01:01', 'HLA-DRB1*15:01:01:02', 'HLA-DRB1*15:01:01:03', 'HLA-DRB1*15:01:01:04', 'HLA-DRB1*15:02:01', 'HLA-DRB1*15:03:01:01', 'HLA-DRB1*15:03:01:02', 'HLA-DRB1*16:02:01']
    lims_contigs: "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,
      chrY,
      chrM,
      chrUn_GL000220v1,
      chr22_KI270733v1_random,
      chrUn_KN707925v1_decoy,
      chr14_KI270726v1_random,
      chrUn_JTFH01000119v1_decoy,
      chrUn_JTFH01000204v1_decoy,
      chrUn_JTFH01000678v1_decoy,
      chrUn_JTFH01000497v1_decoy,
      chrUn_KN707927v1_decoy,
      chrUn_JTFH01000562v1_decoy,
      chrUn_JTFH01000659v1_decoy,
      chrUn_JTFH01001134v1_decoy,
      chrUn_JTFH01000888v1_decoy,
      chrUn_JTFH01000695v1_decoy,
      chrUn_JTFH01000697v1_decoy"
    calling_contigs:
      # Contigs in the genome build that should be considered for variant calling
      # Note that chrM is not included in this list because the mitochrondria
      # should be analyzed separately.
      - {"contig": chr1, "length": 248956422}
      - {"contig": chr2, "length": 242193529}
      - {"contig": chr3, "length": 198295559}
      - {"contig": chr4, "length": 190214555}
      - {"contig": chr5, "length": 181538259}
      - {"contig": chr6, "length": 170805979}
      - {"contig": chr7, "length": 159345973}
      - {"contig": chr8, "length": 145138636}
      - {"contig": chr9, "length": 138394717}
      - {"contig": chr10, "length": 133797422}
      - {"contig": chr11, "length": 135086622}
      - {"contig": chr12, "length": 133275309}
      - {"contig": chr13, "length": 114364328}
      - {"contig": chr14, "length": 107043718}
      - {"contig": chr15, "length": 101991189}
      - {"contig": chr16, "length": 90338345}
      - {"contig": chr17, "length": 83257441}
      - {"contig": chr18, "length": 80373285}
      - {"contig": chr19, "length": 58617616}
      - {"contig": chr20, "length": 64444167}
      - {"contig": chr21, "length": 46709983}
      - {"contig": chr22, "length": 50818468}
      - {"contig": chrX, "length": 156040895}
      - {"contig": chrY, "length": 57227415}
      - {"contig": "chr1_KI270706v1_random", "length": 175055}
      - {"contig": "chr1_KI270707v1_random", "length": 32032}
      - {"contig": "chr1_KI270708v1_random", "length": 127682}
      - {"contig": "chr1_KI270709v1_random", "length": 66860}
      - {"contig": "chr1_KI270710v1_random", "length": 40176}
      - {"contig": "chr1_KI270711v1_random", "length": 42210}
      - {"contig": "chr1_KI270712v1_random", "length": 176043}
      - {"contig": "chr1_KI270713v1_random", "length": 40745}
      - {"contig": "chr1_KI270714v1_random", "length": 41717}
      - {"contig": "chr2_KI270715v1_random", "length": 161471}
      - {"contig": "chr2_KI270716v1_random", "length": 153799}
      - {"contig": "chr3_GL000221v1_random", "length": 155397}
      - {"contig": "chr4_GL000008v2_random", "length": 209709}
      - {"contig": "chr5_GL000208v1_random", "length": 92689}
      - {"contig": "chr9_KI270717v1_random", "length": 40062}
      - {"contig": "chr9_KI270718v1_random", "length": 38054}
      - {"contig": "chr9_KI270719v1_random", "length": 176845}
      - {"contig": "chr9_KI270720v1_random", "length": 39050}
      - {"contig": "chr11_KI270721v1_random", "length": 100316}
      - {"contig": "chr14_GL000009v2_random", "length": 201709}
      - {"contig": "chr14_GL000225v1_random", "length": 211173}
      - {"contig": "chr14_KI270722v1_random", "length": 194050}
      - {"contig": "chr14_GL000194v1_random", "length": 191469}
      - {"contig": "chr14_KI270723v1_random", "length": 38115}
      - {"contig": "chr14_KI270724v1_random", "length": 39555}
      - {"contig": "chr14_KI270725v1_random", "length": 172810}
      - {"contig": "chr14_KI270726v1_random", "length": 43739}
      - {"contig": "chr15_KI270727v1_random", "length": 448248}
      - {"contig": "chr16_KI270728v1_random", "length": 1872759}
      - {"contig": "chr17_GL000205v2_random", "length": 185591}
      - {"contig": "chr17_KI270729v1_random", "length": 280839}
      - {"contig": "chr17_KI270730v1_random", "length": 112551}
      - {"contig": "chr22_KI270731v1_random", "length": 150754}
      - {"contig": "chr22_KI270732v1_random", "length": 41543}
      - {"contig": "chr22_KI270733v1_random", "length": 179772}
      - {"contig": "chr22_KI270734v1_random", "length": 165050}
      - {"contig": "chr22_KI270735v1_random", "length": 42811}
      - {"contig": "chr22_KI270736v1_random", "length": 181920}
      - {"contig": "chr22_KI270737v1_random", "length": 103838}
      - {"contig": "chr22_KI270738v1_random", "length": 99375}
      - {"contig": "chr22_KI270739v1_random", "length": 73985}
      - {"contig": "chrY_KI270740v1_random", "length": 37240}
      - {"contig": "chrUn_KI270302v1", "length": 2274}
      - {"contig": "chrUn_KI270304v1", "length": 2165}
      - {"contig": "chrUn_KI270303v1", "length": 1942}
      - {"contig": "chrUn_KI270305v1", "length": 1472}
      - {"contig": "chrUn_KI270322v1", "length": 21476}
      - {"contig": "chrUn_KI270320v1", "length": 4416}
      - {"contig": "chrUn_KI270310v1", "length": 1201}
      - {"contig": "chrUn_KI270316v1", "length": 1444}
      - {"contig": "chrUn_KI270315v1", "length": 2276}
      - {"contig": "chrUn_KI270312v1", "length": 998}
      - {"contig": "chrUn_KI270311v1", "length": 12399}
      - {"contig": "chrUn_KI270317v1", "length": 37690}
      - {"contig": "chrUn_KI270412v1", "length": 1179}
      - {"contig": "chrUn_KI270411v1", "length": 2646}
      - {"contig": "chrUn_KI270414v1", "length": 2489}
      - {"contig": "chrUn_KI270419v1", "length": 1029}
      - {"contig": "chrUn_KI270418v1", "length": 2145}
      - {"contig": "chrUn_KI270420v1", "length": 2321}
      - {"contig": "chrUn_KI270424v1", "length": 2140}
      - {"contig": "chrUn_KI270417v1", "length": 2043}
      - {"contig": "chrUn_KI270422v1", "length": 1445}
      - {"contig": "chrUn_KI270423v1", "length": 981}
      - {"contig": "chrUn_KI270425v1", "length": 1884}
      - {"contig": "chrUn_KI270429v1", "length": 1361}
      - {"contig": "chrUn_KI270442v1", "length": 392061}
      - {"contig": "chrUn_KI270466v1", "length": 1233}
      - {"contig": "chrUn_KI270465v1", "length": 1774}
      - {"contig": "chrUn_KI270467v1", "length": 3920}
      - {"contig": "chrUn_KI270435v1", "length": 92983}
      - {"contig": "chrUn_KI270438v1", "length": 112505}
      - {"contig": "chrUn_KI270468v1", "length": 4055}
      - {"contig": "chrUn_KI270510v1", "length": 2415}
      - {"contig": "chrUn_KI270509v1", "length": 2318}
      - {"contig": "chrUn_KI270518v1", "length": 2186}
      - {"contig": "chrUn_KI270508v1", "length": 1951}
      - {"contig": "chrUn_KI270516v1", "length": 1300}
      - {"contig": "chrUn_KI270512v1", "length": 22689}
      - {"contig": "chrUn_KI270519v1", "length": 138126}
      - {"contig": "chrUn_KI270522v1", "length": 5674}
      - {"contig": "chrUn_KI270511v1", "length": 8127}
      - {"contig": "chrUn_KI270515v1", "length": 6361}
      - {"contig": "chrUn_KI270507v1", "length": 5353}
      - {"contig": "chrUn_KI270517v1", "length": 3253}
      - {"contig": "chrUn_KI270529v1", "length": 1899}
      - {"contig": "chrUn_KI270528v1", "length": 2983}
      - {"contig": "chrUn_KI270530v1", "length": 2168}
      - {"contig": "chrUn_KI270539v1", "length": 993}
      - {"contig": "chrUn_KI270538v1", "length": 91309}
      - {"contig": "chrUn_KI270544v1", "length": 1202}
      - {"contig": "chrUn_KI270548v1", "length": 1599}
      - {"contig": "chrUn_KI270583v1", "length": 1400}
      - {"contig": "chrUn_KI270587v1", "length": 2969}
      - {"contig": "chrUn_KI270580v1", "length": 1553}
      - {"contig": "chrUn_KI270581v1", "length": 7046}
      - {"contig": "chrUn_KI270579v1", "length": 31033}
      - {"contig": "chrUn_KI270589v1", "length": 44474}
      - {"contig": "chrUn_KI270590v1", "length": 4685}
      - {"contig": "chrUn_KI270584v1", "length": 4513}
      - {"contig": "chrUn_KI270582v1", "length": 6504}
      - {"contig": "chrUn_KI270588v1", "length": 6158}
      - {"contig": "chrUn_KI270593v1", "length": 3041}
      - {"contig": "chrUn_KI270591v1", "length": 5796}
      - {"contig": "chrUn_KI270330v1", "length": 1652}
      - {"contig": "chrUn_KI270329v1", "length": 1040}
      - {"contig": "chrUn_KI270334v1", "length": 1368}
      - {"contig": "chrUn_KI270333v1", "length": 2699}
      - {"contig": "chrUn_KI270335v1", "length": 1048}
      - {"contig": "chrUn_KI270338v1", "length": 1428}
      - {"contig": "chrUn_KI270340v1", "length": 1428}
      - {"contig": "chrUn_KI270336v1", "length": 1026}
      - {"contig": "chrUn_KI270337v1", "length": 1121}
      - {"contig": "chrUn_KI270363v1", "length": 1803}
      - {"contig": "chrUn_KI270364v1", "length": 2855}
      - {"contig": "chrUn_KI270362v1", "length": 3530}
      - {"contig": "chrUn_KI270366v1", "length": 8320}
      - {"contig": "chrUn_KI270378v1", "length": 1048}
      - {"contig": "chrUn_KI270379v1", "length": 1045}
      - {"contig": "chrUn_KI270389v1", "length": 1298}
      - {"contig": "chrUn_KI270390v1", "length": 2387}
      - {"contig": "chrUn_KI270387v1", "length": 1537}
      - {"contig": "chrUn_KI270395v1", "length": 1143}
      - {"contig": "chrUn_KI270396v1", "length": 1880}
      - {"contig": "chrUn_KI270388v1", "length": 1216}
      - {"contig": "chrUn_KI270394v1", "length": 970}
      - {"contig": "chrUn_KI270386v1", "length": 1788}
      - {"contig": "chrUn_KI270391v1", "length": 1484}
      - {"contig": "chrUn_KI270383v1", "length": 1750}
      - {"contig": "chrUn_KI270393v1", "length": 1308}
      - {"contig": "chrUn_KI270384v1", "length": 1658}
      - {"contig": "chrUn_KI270392v1", "length": 971}
      - {"contig": "chrUn_KI270381v1", "length": 1930}
      - {"contig": "chrUn_KI270385v1", "length": 990}
      - {"contig": "chrUn_KI270382v1", "length": 4215}
      - {"contig": "chrUn_KI270376v1", "length": 1136}
      - {"contig": "chrUn_KI270374v1", "length": 2656}
      - {"contig": "chrUn_KI270372v1", "length": 1650}
      - {"contig": "chrUn_KI270373v1", "length": 1451}
      - {"contig": "chrUn_KI270375v1", "length": 2378}
      - {"contig": "chrUn_KI270371v1", "length": 2805}
      - {"contig": "chrUn_KI270448v1", "length": 7992}
      - {"contig": "chrUn_KI270521v1", "length": 7642}
      - {"contig": "chrUn_GL000195v1", "length": 182896}
      - {"contig": "chrUn_GL000219v1", "length": 179198}
      - {"contig": "chrUn_GL000220v1", "length": 161802}
      - {"contig": "chrUn_GL000224v1", "length": 179693}
      - {"contig": "chrUn_KI270741v1", "length": 157432}
      - {"contig": "chrUn_GL000226v1", "length": 15008}
      - {"contig": "chrUn_GL000213v1", "length": 164239}
      - {"contig": "chrUn_KI270743v1", "length": 210658}
      - {"contig": "chrUn_KI270744v1", "length": 168472}
      - {"contig": "chrUn_KI270745v1", "length": 41891}
      - {"contig": "chrUn_KI270746v1", "length": 66486}
      - {"contig": "chrUn_KI270747v1", "length": 198735}
      - {"contig": "chrUn_KI270748v1", "length": 93321}
      - {"contig": "chrUn_KI270749v1", "length": 158759}
      - {"contig": "chrUn_KI270750v1", "length": 148850}
      - {"contig": "chrUn_KI270751v1", "length": 150742}
      - {"contig": "chrUn_KI270752v1", "length": 27745}
      - {"contig": "chrUn_KI270753v1", "length": 62944}
      - {"contig": "chrUn_KI270754v1", "length": 40191}
      - {"contig": "chrUn_KI270755v1", "length": 36723}
      - {"contig": "chrUn_KI270756v1", "length": 79590}
      - {"contig": "chrUn_KI270757v1", "length": 71251}
      - {"contig": "chrUn_GL000214v1", "length": 137718}
      - {"contig": "chrUn_KI270742v1", "length": 186739}
      - {"contig": "chrUn_GL000216v2", "length": 176608}
      - {"contig": "chrUn_GL000218v1", "length": 161147}
    calling_intervals:
      # Calling contigs broken down into smaller batches of intervals. These intervals
      # are taken from GATK Resource Bundle and describe regions that can be safely
      # called independently for SNP/small indel genotyping.
      # Removed the following interval batch as both of the intervals completely overlap with an interval in the ENCODE blacklist
      # chr3:90568829-90722458
      # chr3:90772459-91249905
      - - {"contig": "chr1", "length": 197665, "start": 10001, "stop": 207666}
        - {"contig": "chr1", "length": 40301, "start": 257667, "stop": 297968}
        - {"contig": "chr1", "length": 188019, "start": 347969, "stop": 535988}
        - {"contig": "chr1", "length": 2116792, "start": 585989, "stop": 2702781}
        - {"contig": "chr1", "length": 10208093, "start": 2746291, "stop": 12954384}
        - {"contig": "chr1", "length": 3794778, "start": 13004385, "stop": 16799163}
        - {"contig": "chr1", "length": 12703069, "start": 16849164, "stop": 29552233}
      - - {"contig": "chr1", "length": 92422623, "start": 29553836, "stop": 121976459}
        - {"contig": "chr1", "length": 2951484, "start": 122026460, "stop": 124977944}
        - {"contig": "chr1", "length": 151919, "start": 124978327, "stop": 125130246}
        - {"contig": "chr1", "length": 39499, "start": 125131848, "stop": 125171347}
        - {"contig": "chr1", "length": 11003, "start": 125173584, "stop": 125184587}
      - - {"contig": "chr1", "length": 80374347, "start": 143184588, "stop": 223558935}
        - {"contig": "chr1", "length": 4949428, "start": 223608936, "stop": 228558364}
      - - {"contig": "chr1", "length": 20338057, "start": 228608365, "stop": 248946422}
        - {"contig": "chr2", "length": 16135118, "start": 10001, "stop": 16145119}
        - {"contig": "chr2", "length": 16721010, "start": 16146120, "stop": 32867130}
        - {"contig": "chr2", "length": 48494, "start": 32868131, "stop": 32916625}
      - - {"contig": "chr2", "length": 56413053, "start": 32917626, "stop": 89330679}
        - {"contig": "chr2", "length": 155312, "start": 89530680, "stop": 89685992}
        - {"contig": "chr2", "length": 648518, "start": 89753993, "stop": 90402511}
        - {"contig": "chr2", "length": 735633, "start": 91402512, "stop": 92138145}
        - {"contig": "chr2", "length": 1902411, "start": 92188146, "stop": 94090557}
        - {"contig": "chr2", "length": 152457, "start": 94140558, "stop": 94293015}
        - {"contig": "chr2", "length": 2943602, "start": 94496016, "stop": 97439618}
      - - {"contig": "chr2", "length": 141414040, "start": 97489619, "stop": 238903659}
      - - {"contig": "chr2", "length": 3279481, "start": 238904048, "stop": 242183529}
      - - {"contig": "chr3", "length": 90555294, "start": 10001, "stop": 90565295}
      - - {"contig": "chr3", "length": 1468, "start": 91256422, "stop": 91257890}
        - {"contig": "chr3", "length": 5200, "start": 91260181, "stop": 91265381}
        - {"contig": "chr3", "length": 5180, "start": 91276995, "stop": 91282175}
        - {"contig": "chr3", "length": 2187625, "start": 91282735, "stop": 93470360}
        - {"contig": "chr3", "length": 184773, "start": 93470801, "stop": 93655574}
      - - {"contig": "chr3", "length": 104529984, "start": 93705575, "stop": 198235559}
      - - {"contig": "chr4", "length": 1419357, "start": 10001, "stop": 1429358}
        - {"contig": "chr4", "length": 1587, "start": 1434207, "stop": 1435794}
        - {"contig": "chr4", "length": 7355924, "start": 1441553, "stop": 8797477}
        - {"contig": "chr4", "length": 456438, "start": 8816478, "stop": 9272916}
        - {"contig": "chr4", "length": 22496378, "start": 9322917, "stop": 31819295}
        - {"contig": "chr4", "length": 1000446, "start": 31832570, "stop": 32833016}
        - {"contig": "chr4", "length": 16497907, "start": 32839017, "stop": 49336924}
        - {"contig": "chr4", "length": 171175, "start": 49486925, "stop": 49658100}
        - {"contig": "chr4", "length": 2035850, "start": 49708101, "stop": 51743951}
        - {"contig": "chr4", "length": 7084841, "start": 51793952, "stop": 58878793}
      - - {"contig": "chr4", "length": 131201739, "start": 58921382, "stop": 190123121}
      - - {"contig": "chr4", "length": 31433, "start": 190173122, "stop": 190204555}
        - {"contig": "chr5", "length": 17520547, "start": 10001, "stop": 17530548}
        - {"contig": "chr5", "length": 28855351, "start": 17580549, "stop": 46435900}
        - {"contig": "chr5", "length": 583261, "start": 46485901, "stop": 47069162}
        - {"contig": "chr5", "length": 6002, "start": 47073731, "stop": 47079733}
        - {"contig": "chr5", "length": 218504, "start": 47082081, "stop": 47300585}
        - {"contig": "chr5", "length": 2997, "start": 47306087, "stop": 47309084}
        - {"contig": "chr5", "length": 1450, "start": 49591470, "stop": 49592920}
        - {"contig": "chr5", "length": 3807, "start": 49599324, "stop": 49603131}
        - {"contig": "chr5", "length": 2006, "start": 49609715, "stop": 49611721}
        - {"contig": "chr5", "length": 6897, "start": 49612097, "stop": 49618994}
        - {"contig": "chr5", "length": 6559, "start": 49621606, "stop": 49628165}
        - {"contig": "chr5", "length": 3063, "start": 49630730, "stop": 49633793}
        - {"contig": "chr5", "length": 8757, "start": 49641816, "stop": 49650573}
        - {"contig": "chr5", "length": 5609, "start": 49656262, "stop": 49661871}
        - {"contig": "chr5", "length": 393633, "start": 49666174, "stop": 50059807}
      - - {"contig": "chr5", "length": 89342851, "start": 50109808, "stop": 139452659}
      - - {"contig": "chr5", "length": 16306664, "start": 139453660, "stop": 155760324}
        - {"contig": "chr5", "length": 25716934, "start": 155761325, "stop": 181478259}
        - {"contig": "chr6", "length": 58393887, "start": 60001, "stop": 58453888}
        - {"contig": "chr6", "length": 1276045, "start": 58553889, "stop": 59829934}
      - - {"contig": "chr6", "length": 1127094, "start": 60229935, "stop": 61357029}
        - {"contig": "chr6", "length": 7487, "start": 61363067, "stop": 61370554}
        - {"contig": "chr6", "length": 33649417, "start": 61371373, "stop": 95020790}
      - - {"contig": "chr6", "length": 72520602, "start": 95070791, "stop": 167591393}
        - {"contig": "chr6", "length": 3104585, "start": 167641394, "stop": 170745979}
        - {"contig": "chr7", "length": 227845, "start": 10001, "stop": 237846}
      - - {"contig": "chr7", "length": 57879410, "start": 240243, "stop": 58119653}
        - {"contig": "chr7", "length": 2658580, "start": 58169654, "stop": 60828234}
        - {"contig": "chr7", "length": 449553, "start": 60878235, "stop": 61327788}
        - {"contig": "chr7", "length": 150231, "start": 61377789, "stop": 61528020}
        - {"contig": "chr7", "length": 386148, "start": 61578021, "stop": 61964169}
        - {"contig": "chr7", "length": 9040, "start": 61967064, "stop": 61976104}
        - {"contig": "chr7", "length": 430674, "start": 62026105, "stop": 62456779}
      - - {"contig": "chr7", "length": 81144024, "start": 62506780, "stop": 143650804}
        - {"contig": "chr7", "length": 15635168, "start": 143700805, "stop": 159335973}
      - - {"contig": "chr8", "length": 7557126, "start": 60001, "stop": 7617127}
        - {"contig": "chr8", "length": 4567217, "start": 7667128, "stop": 12234345}
        - {"contig": "chr8", "length": 31699398, "start": 12284346, "stop": 43983744}
        - {"contig": "chr8", "length": 1843520, "start": 44033745, "stop": 45877265}
        - {"contig": "chr8", "length": 39736956, "start": 45927266, "stop": 85664222}
      - - {"contig": "chr8", "length": 59364413, "start": 85714223, "stop": 145078636}
        - {"contig": "chr9", "length": 41215985, "start": 10001, "stop": 41225986}
        - {"contig": "chr9", "length": 8373, "start": 41229379, "stop": 41237752}
      - - {"contig": "chr9", "length": 1983662, "start": 41238505, "stop": 43222167}
        - {"contig": "chr9", "length": 27122, "start": 43236168, "stop": 43263290}
        - {"contig": "chr9", "length": 7123, "start": 43263821, "stop": 43270944}
        - {"contig": "chr9", "length": 1312, "start": 43274936, "stop": 43276248}
        - {"contig": "chr9", "length": 4865, "start": 43276458, "stop": 43281323}
        - {"contig": "chr9", "length": 49217, "start": 43282957, "stop": 43332174}
        - {"contig": "chr9", "length": 37135, "start": 43333270, "stop": 43370405}
        - {"contig": "chr9", "length": 6127, "start": 43371326, "stop": 43377453}
        - {"contig": "chr9", "length": 2136278, "start": 43382280, "stop": 45518558}
        - {"contig": "chr9", "length": 169873, "start": 60518559, "stop": 60688432}
        - {"contig": "chr9", "length": 41088, "start": 60738433, "stop": 60779521}
        - {"contig": "chr9", "length": 174365, "start": 60829522, "stop": 61003887}
        - {"contig": "chr9", "length": 178078, "start": 61053888, "stop": 61231966}
        - {"contig": "chr9", "length": 186841, "start": 61281967, "stop": 61468808}
        - {"contig": "chr9", "length": 216559, "start": 61518809, "stop": 61735368}
        - {"contig": "chr9", "length": 364369, "start": 61785369, "stop": 62149738}
        - {"contig": "chr9", "length": 499093, "start": 62249739, "stop": 62748832}
        - {"contig": "chr9", "length": 159538, "start": 62798833, "stop": 62958371}
        - {"contig": "chr9", "length": 194490, "start": 63008372, "stop": 63202862}
        - {"contig": "chr9", "length": 239401, "start": 63252863, "stop": 63492264}
        - {"contig": "chr9", "length": 376182, "start": 63542265, "stop": 63918447}
        - {"contig": "chr9", "length": 166565, "start": 63968448, "stop": 64135013}
        - {"contig": "chr9", "length": 30148, "start": 64185014, "stop": 64215162}
        - {"contig": "chr9", "length": 682961, "start": 64315163, "stop": 64998124}
        - {"contig": "chr9", "length": 31957, "start": 65048125, "stop": 65080082}
        - {"contig": "chr9", "length": 195040, "start": 65130083, "stop": 65325123}
        - {"contig": "chr9", "length": 220067, "start": 65375124, "stop": 65595191}
        - {"contig": "chr9", "length": 746195, "start": 65645192, "stop": 66391387}
        - {"contig": "chr9", "length": 1329164, "start": 66591388, "stop": 67920552}
        - {"contig": "chr9", "length": 65962539, "start": 68220553, "stop": 134183092}
        - {"contig": "chr9", "length": 4149180, "start": 134185537, "stop": 138334717}
      - - {"contig": "chr10", "length": 38519906, "start": 10001, "stop": 38529907}
        - {"contig": "chr10", "length": 332697, "start": 38573339, "stop": 38906036}
        - {"contig": "chr10", "length": 1857, "start": 38911581, "stop": 38913438}
        - {"contig": "chr10", "length": 311648, "start": 38918270, "stop": 39229918}
        - {"contig": "chr10", "length": 179655, "start": 39230137, "stop": 39409792}
        - {"contig": "chr10", "length": 175049, "start": 39410238, "stop": 39585287}
        - {"contig": "chr10", "length": 2577, "start": 39590436, "stop": 39593013}
        - {"contig": "chr10", "length": 5263, "start": 39597436, "stop": 39602699}
        - {"contig": "chr10", "length": 7099, "start": 39606090, "stop": 39613189}
        - {"contig": "chr10", "length": 6734, "start": 39615619, "stop": 39622353}
        - {"contig": "chr10", "length": 11407, "start": 39625275, "stop": 39636682}
        - {"contig": "chr10", "length": 1906838, "start": 39686683, "stop": 41593521}
        - {"contig": "chr10", "length": 222743, "start": 41693522, "stop": 41916265}
        - {"contig": "chr10", "length": 5714102, "start": 42066266, "stop": 47780368}
      - - {"contig": "chr10", "length": 76250831, "start": 47870369, "stop": 124121200}
        - {"contig": "chr10", "length": 9568963, "start": 124121503, "stop": 133690466}
        - {"contig": "chr10", "length": 46955, "start": 133740467, "stop": 133787422}
      - - {"contig": "chr11", "length": 50761347, "start": 60001, "stop": 50821348}
        - {"contig": "chr11", "length": 3346725, "start": 51078349, "stop": 54425074}
        - {"contig": "chr11", "length": 16430621, "start": 54525075, "stop": 70955696}
        - {"contig": "chr11", "length": 16922505, "start": 71055697, "stop": 87978202}
      - - {"contig": "chr11", "length": 47073725, "start": 88002897, "stop": 135076622}
        - {"contig": "chr12", "length": 7073649, "start": 10001, "stop": 7083650}
        - {"contig": "chr12", "length": 27634756, "start": 7084651, "stop": 34719407}
        - {"contig": "chr12", "length": 52881, "start": 34769408, "stop": 34822289}
        - {"contig": "chr12", "length": 2356014, "start": 34829238, "stop": 37185252}
        - {"contig": "chr12", "length": 5691, "start": 37235253, "stop": 37240944}
        - {"contig": "chr12", "length": 9615, "start": 37245717, "stop": 37255332}
        - {"contig": "chr12", "length": 122795, "start": 37257056, "stop": 37379851}
      - - {"contig": "chr12", "length": 94842901, "start": 37380461, "stop": 132223362}
        - {"contig": "chr12", "length": 1040946, "start": 132224363, "stop": 133265309}
        - {"contig": "chr13", "length": 2051247, "start": 16000001, "stop": 18051248}
        - {"contig": "chr13", "length": 186857, "start": 18171249, "stop": 18358106}
      - - {"contig": "chr13", "length": 67794872, "start": 18408107, "stop": 86202979}
        - {"contig": "chr13", "length": 25450875, "start": 86252980, "stop": 111703855}
        - {"contig": "chr13", "length": 39585, "start": 111753856, "stop": 111793441}
        - {"contig": "chr13", "length": 1829578, "start": 111843442, "stop": 113673020}
        - {"contig": "chr13", "length": 631307, "start": 113723021, "stop": 114354328}
        - {"contig": "chr14", "length": 31338, "start": 16022638, "stop": 16053976}
        - {"contig": "chr14", "length": 7217, "start": 16054460, "stop": 16061677}
        - {"contig": "chr14", "length": 24631, "start": 16061994, "stop": 16086625}
        - {"contig": "chr14", "length": 15813, "start": 16089563, "stop": 16105376}
        - {"contig": "chr14", "length": 17625, "start": 16113233, "stop": 16130858}
        - {"contig": "chr14", "length": 7191, "start": 16133336, "stop": 16140527}
        - {"contig": "chr14", "length": 4184, "start": 16400164, "stop": 16404348}
        - {"contig": "chr14", "length": 489120, "start": 18223524, "stop": 18712644}
        - {"contig": "chr14", "length": 649068, "start": 18862645, "stop": 19511713}
      - - {"contig": "chr14", "length": 87272004, "start": 19611714, "stop": 106883718}
        - {"contig": "chr15", "length": 2725253, "start": 17000001, "stop": 19725254}
        - {"contig": "chr15", "length": 914049, "start": 19775255, "stop": 20689304}
        - {"contig": "chr15", "length": 463743, "start": 20729747, "stop": 21193490}
        - {"contig": "chr15", "length": 536411, "start": 21242091, "stop": 21778502}
        - {"contig": "chr15", "length": 479739, "start": 21828503, "stop": 22308242}
        - {"contig": "chr15", "length": 868631, "start": 22358243, "stop": 23226874}
      - - {"contig": "chr15", "length": 60993191, "start": 23276875, "stop": 84270066}
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        - {"contig": "chrUn_KI270420v1", "length": 2321, "start": 1, "stop": 2321}
        - {"contig": "chrUn_KI270424v1", "length": 2140, "start": 1, "stop": 2140}
        - {"contig": "chrUn_KI270417v1", "length": 2043, "start": 1, "stop": 2043}
        - {"contig": "chrUn_KI270422v1", "length": 1445, "start": 1, "stop": 1445}
        - {"contig": "chrUn_KI270423v1", "length": 981, "start": 1, "stop": 981}
        - {"contig": "chrUn_KI270425v1", "length": 1884, "start": 1, "stop": 1884}
        - {"contig": "chrUn_KI270429v1", "length": 1361, "start": 1, "stop": 1361}
      - - {"contig": "chrUn_KI270442v1", "length": 392061, "start": 1, "stop": 392061}
        - {"contig": "chrUn_KI270466v1", "length": 1233, "start": 1, "stop": 1233}
        - {"contig": "chrUn_KI270465v1", "length": 1774, "start": 1, "stop": 1774}
        - {"contig": "chrUn_KI270467v1", "length": 3920, "start": 1, "stop": 3920}
        - {"contig": "chrUn_KI270435v1", "length": 92983, "start": 1, "stop": 92983}
        - {"contig": "chrUn_KI270438v1", "length": 112505, "start": 1, "stop": 112505}
        - {"contig": "chrUn_KI270468v1", "length": 4055, "start": 1, "stop": 4055}
        - {"contig": "chrUn_KI270510v1", "length": 2415, "start": 1, "stop": 2415}
        - {"contig": "chrUn_KI270509v1", "length": 2318, "start": 1, "stop": 2318}
        - {"contig": "chrUn_KI270518v1", "length": 2186, "start": 1, "stop": 2186}
        - {"contig": "chrUn_KI270508v1", "length": 1951, "start": 1, "stop": 1951}
        - {"contig": "chrUn_KI270516v1", "length": 1300, "start": 1, "stop": 1300}
        - {"contig": "chrUn_KI270512v1", "length": 22689, "start": 1, "stop": 22689}
        - {"contig": "chrUn_KI270519v1", "length": 138126, "start": 1, "stop": 138126}
        - {"contig": "chrUn_KI270522v1", "length": 5674, "start": 1, "stop": 5674}
        - {"contig": "chrUn_KI270511v1", "length": 8127, "start": 1, "stop": 8127}
        - {"contig": "chrUn_KI270515v1", "length": 6361, "start": 1, "stop": 6361}
        - {"contig": "chrUn_KI270507v1", "length": 5353, "start": 1, "stop": 5353}
        - {"contig": "chrUn_KI270517v1", "length": 3253, "start": 1, "stop": 3253}
        - {"contig": "chrUn_KI270529v1", "length": 1899, "start": 1, "stop": 1899}
        - {"contig": "chrUn_KI270528v1", "length": 2983, "start": 1, "stop": 2983}
        - {"contig": "chrUn_KI270530v1", "length": 2168, "start": 1, "stop": 2168}
        - {"contig": "chrUn_KI270539v1", "length": 993, "start": 1, "stop": 993}
      - - {"contig": "chrUn_KI270538v1", "length": 91309, "start": 1, "stop": 91309}
        - {"contig": "chrUn_KI270544v1", "length": 1202, "start": 1, "stop": 1202}
        - {"contig": "chrUn_KI270548v1", "length": 1599, "start": 1, "stop": 1599}
        - {"contig": "chrUn_KI270583v1", "length": 1400, "start": 1, "stop": 1400}
        - {"contig": "chrUn_KI270587v1", "length": 2969, "start": 1, "stop": 2969}
        - {"contig": "chrUn_KI270580v1", "length": 1553, "start": 1, "stop": 1553}
        - {"contig": "chrUn_KI270581v1", "length": 7046, "start": 1, "stop": 7046}
        - {"contig": "chrUn_KI270579v1", "length": 31033, "start": 1, "stop": 31033}
        - {"contig": "chrUn_KI270589v1", "length": 44474, "start": 1, "stop": 44474}
        - {"contig": "chrUn_KI270590v1", "length": 4685, "start": 1, "stop": 4685}
        - {"contig": "chrUn_KI270584v1", "length": 4513, "start": 1, "stop": 4513}
        - {"contig": "chrUn_KI270582v1", "length": 6504, "start": 1, "stop": 6504}
        - {"contig": "chrUn_KI270588v1", "length": 6158, "start": 1, "stop": 6158}
        - {"contig": "chrUn_KI270593v1", "length": 3041, "start": 1, "stop": 3041}
        - {"contig": "chrUn_KI270591v1", "length": 5796, "start": 1, "stop": 5796}
        - {"contig": "chrUn_KI270330v1", "length": 1652, "start": 1, "stop": 1652}
        - {"contig": "chrUn_KI270329v1", "length": 1040, "start": 1, "stop": 1040}
        - {"contig": "chrUn_KI270334v1", "length": 1368, "start": 1, "stop": 1368}
        - {"contig": "chrUn_KI270333v1", "length": 2699, "start": 1, "stop": 2699}
        - {"contig": "chrUn_KI270335v1", "length": 1048, "start": 1, "stop": 1048}
        - {"contig": "chrUn_KI270338v1", "length": 1428, "start": 1, "stop": 1428}
        - {"contig": "chrUn_KI270340v1", "length": 1428, "start": 1, "stop": 1428}
        - {"contig": "chrUn_KI270336v1", "length": 1026, "start": 1, "stop": 1026}
        - {"contig": "chrUn_KI270337v1", "length": 1121, "start": 1, "stop": 1121}
        - {"contig": "chrUn_KI270363v1", "length": 1803, "start": 1, "stop": 1803}
        - {"contig": "chrUn_KI270364v1", "length": 2855, "start": 1, "stop": 2855}
        - {"contig": "chrUn_KI270362v1", "length": 3530, "start": 1, "stop": 3530}
        - {"contig": "chrUn_KI270366v1", "length": 8320, "start": 1, "stop": 8320}
        - {"contig": "chrUn_KI270378v1", "length": 1048, "start": 1, "stop": 1048}
        - {"contig": "chrUn_KI270379v1", "length": 1045, "start": 1, "stop": 1045}
        - {"contig": "chrUn_KI270389v1", "length": 1298, "start": 1, "stop": 1298}
        - {"contig": "chrUn_KI270390v1", "length": 2387, "start": 1, "stop": 2387}
        - {"contig": "chrUn_KI270387v1", "length": 1537, "start": 1, "stop": 1537}
        - {"contig": "chrUn_KI270395v1", "length": 1143, "start": 1, "stop": 1143}
      - - {"contig": "chrUn_KI270396v1", "length": 1880, "start": 1, "stop": 1880}
        - {"contig": "chrUn_KI270388v1", "length": 1216, "start": 1, "stop": 1216}
        - {"contig": "chrUn_KI270394v1", "length": 970, "start": 1, "stop": 970}
        - {"contig": "chrUn_KI270386v1", "length": 1788, "start": 1, "stop": 1788}
        - {"contig": "chrUn_KI270391v1", "length": 1484, "start": 1, "stop": 1484}
        - {"contig": "chrUn_KI270383v1", "length": 1750, "start": 1, "stop": 1750}
        - {"contig": "chrUn_KI270393v1", "length": 1308, "start": 1, "stop": 1308}
        - {"contig": "chrUn_KI270384v1", "length": 1658, "start": 1, "stop": 1658}
        - {"contig": "chrUn_KI270392v1", "length": 971, "start": 1, "stop": 971}
        - {"contig": "chrUn_KI270381v1", "length": 1930, "start": 1, "stop": 1930}
        - {"contig": "chrUn_KI270385v1", "length": 990, "start": 1, "stop": 990}
        - {"contig": "chrUn_KI270382v1", "length": 4215, "start": 1, "stop": 4215}
        - {"contig": "chrUn_KI270376v1", "length": 1136, "start": 1, "stop": 1136}
        - {"contig": "chrUn_KI270374v1", "length": 2656, "start": 1, "stop": 2656}
        - {"contig": "chrUn_KI270372v1", "length": 1650, "start": 1, "stop": 1650}
        - {"contig": "chrUn_KI270373v1", "length": 1451, "start": 1, "stop": 1451}
        - {"contig": "chrUn_KI270375v1", "length": 2378, "start": 1, "stop": 2378}
        - {"contig": "chrUn_KI270371v1", "length": 2805, "start": 1, "stop": 2805}
        - {"contig": "chrUn_KI270448v1", "length": 7992, "start": 1, "stop": 7992}
        - {"contig": "chrUn_KI270521v1", "length": 7642, "start": 1, "stop": 7642}
        - {"contig": "chrUn_GL000195v1", "length": 182896, "start": 1, "stop": 182896}
        - {"contig": "chrUn_GL000219v1", "length": 179198, "start": 1, "stop": 179198}
        - {"contig": "chrUn_GL000220v1", "length": 161802, "start": 1, "stop": 161802}
        - {"contig": "chrUn_GL000224v1", "length": 179693, "start": 1, "stop": 179693}
        - {"contig": "chrUn_KI270741v1", "length": 157432, "start": 1, "stop": 157432}
        - {"contig": "chrUn_GL000226v1", "length": 15008, "start": 1, "stop": 15008}
        - {"contig": "chrUn_GL000213v1", "length": 164239, "start": 1, "stop": 164239}
      - - {"contig": "chrUn_KI270743v1", "length": 210658, "start": 1, "stop": 210658}
        - {"contig": "chrUn_KI270744v1", "length": 168472, "start": 1, "stop": 168472}
        - {"contig": "chrUn_KI270745v1", "length": 41891, "start": 1, "stop": 41891}
        - {"contig": "chrUn_KI270746v1", "length": 66486, "start": 1, "stop": 66486}
        - {"contig": "chrUn_KI270747v1", "length": 198735, "start": 1, "stop": 198735}
        - {"contig": "chrUn_KI270748v1", "length": 93321, "start": 1, "stop": 93321}
        - {"contig": "chrUn_KI270749v1", "length": 158759, "start": 1, "stop": 158759}
        - {"contig": "chrUn_KI270750v1", "length": 148850, "start": 1, "stop": 148850}
        - {"contig": "chrUn_KI270751v1", "length": 150742, "start": 1, "stop": 150742}
        - {"contig": "chrUn_KI270752v1", "length": 27745, "start": 1, "stop": 27745}
        - {"contig": "chrUn_KI270753v1", "length": 62944, "start": 1, "stop": 62944}
        - {"contig": "chrUn_KI270754v1", "length": 40191, "start": 1, "stop": 40191}
        - {"contig": "chrUn_KI270755v1", "length": 36723, "start": 1, "stop": 36723}
        - {"contig": "chrUn_KI270756v1", "length": 79590, "start": 1, "stop": 79590}
        - {"contig": "chrUn_KI270757v1", "length": 71251, "start": 1, "stop": 71251}
        - {"contig": "chrUn_GL000214v1", "length": 137718, "start": 1, "stop": 137718}
        - {"contig": "chrUn_KI270742v1", "length": 186739, "start": 1, "stop": 186739}
        - {"contig": "chrUn_GL000216v2", "length": 176608, "start": 1, "stop": 176608}
        - {"contig": "chrUn_GL000218v1", "length": 161147, "start": 1, "stop": 161147}
    primary_contig_calling_intervals:
      # Calling contigs broken down into smaller batches of intervals. These intervals
      # are taken from GATK Resource Bundle and describe regions that can be safely
      # called independently for SNP/small indel genotyping.
      # These intervals are from the primary contigs and have had the following interval batch removed
      # as both of the intervals completely overlap with an interval in the ENCODE blacklist
      # chr3:90568829-90722458
      # chr3:90772459-91249905
      - - {"contig": "chr1", "length": 197665, "start": 10001, "stop": 207666}
        - {"contig": "chr1", "length": 40301, "start": 257667, "stop": 297968}
        - {"contig": "chr1", "length": 188019, "start": 347969, "stop": 535988}
        - {"contig": "chr1", "length": 2116792, "start": 585989, "stop": 2702781}
        - {"contig": "chr1", "length": 10208093, "start": 2746291, "stop": 12954384}
        - {"contig": "chr1", "length": 3794778, "start": 13004385, "stop": 16799163}
        - {"contig": "chr1", "length": 12703069, "start": 16849164, "stop": 29552233}
      - - {"contig": "chr1", "length": 92422623, "start": 29553836, "stop": 121976459}
        - {"contig": "chr1", "length": 2951484, "start": 122026460, "stop": 124977944}
        - {"contig": "chr1", "length": 151919, "start": 124978327, "stop": 125130246}
        - {"contig": "chr1", "length": 39499, "start": 125131848, "stop": 125171347}
        - {"contig": "chr1", "length": 11003, "start": 125173584, "stop": 125184587}
      - - {"contig": "chr1", "length": 80374347, "start": 143184588, "stop": 223558935}
        - {"contig": "chr1", "length": 4949428, "start": 223608936, "stop": 228558364}
      - - {"contig": "chr1", "length": 20338057, "start": 228608365, "stop": 248946422}
        - {"contig": "chr2", "length": 16135118, "start": 10001, "stop": 16145119}
        - {"contig": "chr2", "length": 16721010, "start": 16146120, "stop": 32867130}
        - {"contig": "chr2", "length": 48494, "start": 32868131, "stop": 32916625}
      - - {"contig": "chr2", "length": 56413053, "start": 32917626, "stop": 89330679}
        - {"contig": "chr2", "length": 155312, "start": 89530680, "stop": 89685992}
        - {"contig": "chr2", "length": 648518, "start": 89753993, "stop": 90402511}
        - {"contig": "chr2", "length": 735633, "start": 91402512, "stop": 92138145}
        - {"contig": "chr2", "length": 1902411, "start": 92188146, "stop": 94090557}
        - {"contig": "chr2", "length": 152457, "start": 94140558, "stop": 94293015}
        - {"contig": "chr2", "length": 2943602, "start": 94496016, "stop": 97439618}
      - - {"contig": "chr2", "length": 141414040, "start": 97489619, "stop": 238903659}
      - - {"contig": "chr2", "length": 3279481, "start": 238904048, "stop": 242183529}
      - - {"contig": "chr3", "length": 90555294, "start": 10001, "stop": 90565295}
      - - {"contig": "chr3", "length": 1468, "start": 91256422, "stop": 91257890}
        - {"contig": "chr3", "length": 5200, "start": 91260181, "stop": 91265381}
        - {"contig": "chr3", "length": 5180, "start": 91276995, "stop": 91282175}
        - {"contig": "chr3", "length": 2187625, "start": 91282735, "stop": 93470360}
        - {"contig": "chr3", "length": 184773, "start": 93470801, "stop": 93655574}
      - - {"contig": "chr3", "length": 104529984, "start": 93705575, "stop": 198235559}
      - - {"contig": "chr4", "length": 1419357, "start": 10001, "stop": 1429358}
        - {"contig": "chr4", "length": 1587, "start": 1434207, "stop": 1435794}
        - {"contig": "chr4", "length": 7355924, "start": 1441553, "stop": 8797477}
        - {"contig": "chr4", "length": 456438, "start": 8816478, "stop": 9272916}
        - {"contig": "chr4", "length": 22496378, "start": 9322917, "stop": 31819295}
        - {"contig": "chr4", "length": 1000446, "start": 31832570, "stop": 32833016}
        - {"contig": "chr4", "length": 16497907, "start": 32839017, "stop": 49336924}
        - {"contig": "chr4", "length": 171175, "start": 49486925, "stop": 49658100}
        - {"contig": "chr4", "length": 2035850, "start": 49708101, "stop": 51743951}
        - {"contig": "chr4", "length": 7084841, "start": 51793952, "stop": 58878793}
      - - {"contig": "chr4", "length": 131201739, "start": 58921382, "stop": 190123121}
      - - {"contig": "chr4", "length": 31433, "start": 190173122, "stop": 190204555}
        - {"contig": "chr5", "length": 17520547, "start": 10001, "stop": 17530548}
        - {"contig": "chr5", "length": 28855351, "start": 17580549, "stop": 46435900}
        - {"contig": "chr5", "length": 583261, "start": 46485901, "stop": 47069162}
        - {"contig": "chr5", "length": 6002, "start": 47073731, "stop": 47079733}
        - {"contig": "chr5", "length": 218504, "start": 47082081, "stop": 47300585}
        - {"contig": "chr5", "length": 2997, "start": 47306087, "stop": 47309084}
        - {"contig": "chr5", "length": 1450, "start": 49591470, "stop": 49592920}
        - {"contig": "chr5", "length": 3807, "start": 49599324, "stop": 49603131}
        - {"contig": "chr5", "length": 2006, "start": 49609715, "stop": 49611721}
        - {"contig": "chr5", "length": 6897, "start": 49612097, "stop": 49618994}
        - {"contig": "chr5", "length": 6559, "start": 49621606, "stop": 49628165}
        - {"contig": "chr5", "length": 3063, "start": 49630730, "stop": 49633793}
        - {"contig": "chr5", "length": 8757, "start": 49641816, "stop": 49650573}
        - {"contig": "chr5", "length": 5609, "start": 49656262, "stop": 49661871}
        - {"contig": "chr5", "length": 393633, "start": 49666174, "stop": 50059807}
      - - {"contig": "chr5", "length": 89342851, "start": 50109808, "stop": 139452659}
      - - {"contig": "chr5", "length": 16306664, "start": 139453660, "stop": 155760324}
        - {"contig": "chr5", "length": 25716934, "start": 155761325, "stop": 181478259}
        - {"contig": "chr6", "length": 58393887, "start": 60001, "stop": 58453888}
        - {"contig": "chr6", "length": 1276045, "start": 58553889, "stop": 59829934}
      - - {"contig": "chr6", "length": 1127094, "start": 60229935, "stop": 61357029}
        - {"contig": "chr6", "length": 7487, "start": 61363067, "stop": 61370554}
        - {"contig": "chr6", "length": 33649417, "start": 61371373, "stop": 95020790}
      - - {"contig": "chr6", "length": 72520602, "start": 95070791, "stop": 167591393}
        - {"contig": "chr6", "length": 3104585, "start": 167641394, "stop": 170745979}
        - {"contig": "chr7", "length": 227845, "start": 10001, "stop": 237846}
      - - {"contig": "chr7", "length": 57879410, "start": 240243, "stop": 58119653}
        - {"contig": "chr7", "length": 2658580, "start": 58169654, "stop": 60828234}
        - {"contig": "chr7", "length": 449553, "start": 60878235, "stop": 61327788}
        - {"contig": "chr7", "length": 150231, "start": 61377789, "stop": 61528020}
        - {"contig": "chr7", "length": 386148, "start": 61578021, "stop": 61964169}
        - {"contig": "chr7", "length": 9040, "start": 61967064, "stop": 61976104}
        - {"contig": "chr7", "length": 430674, "start": 62026105, "stop": 62456779}
      - - {"contig": "chr7", "length": 81144024, "start": 62506780, "stop": 143650804}
        - {"contig": "chr7", "length": 15635168, "start": 143700805, "stop": 159335973}
      - - {"contig": "chr8", "length": 7557126, "start": 60001, "stop": 7617127}
        - {"contig": "chr8", "length": 4567217, "start": 7667128, "stop": 12234345}
        - {"contig": "chr8", "length": 31699398, "start": 12284346, "stop": 43983744}
        - {"contig": "chr8", "length": 1843520, "start": 44033745, "stop": 45877265}
        - {"contig": "chr8", "length": 39736956, "start": 45927266, "stop": 85664222}
      - - {"contig": "chr8", "length": 59364413, "start": 85714223, "stop": 145078636}
        - {"contig": "chr9", "length": 41215985, "start": 10001, "stop": 41225986}
        - {"contig": "chr9", "length": 8373, "start": 41229379, "stop": 41237752}
      - - {"contig": "chr9", "length": 1983662, "start": 41238505, "stop": 43222167}
        - {"contig": "chr9", "length": 27122, "start": 43236168, "stop": 43263290}
        - {"contig": "chr9", "length": 7123, "start": 43263821, "stop": 43270944}
        - {"contig": "chr9", "length": 1312, "start": 43274936, "stop": 43276248}
        - {"contig": "chr9", "length": 4865, "start": 43276458, "stop": 43281323}
        - {"contig": "chr9", "length": 49217, "start": 43282957, "stop": 43332174}
        - {"contig": "chr9", "length": 37135, "start": 43333270, "stop": 43370405}
        - {"contig": "chr9", "length": 6127, "start": 43371326, "stop": 43377453}
        - {"contig": "chr9", "length": 2136278, "start": 43382280, "stop": 45518558}
        - {"contig": "chr9", "length": 169873, "start": 60518559, "stop": 60688432}
        - {"contig": "chr9", "length": 41088, "start": 60738433, "stop": 60779521}
        - {"contig": "chr9", "length": 174365, "start": 60829522, "stop": 61003887}
        - {"contig": "chr9", "length": 178078, "start": 61053888, "stop": 61231966}
        - {"contig": "chr9", "length": 186841, "start": 61281967, "stop": 61468808}
        - {"contig": "chr9", "length": 216559, "start": 61518809, "stop": 61735368}
        - {"contig": "chr9", "length": 364369, "start": 61785369, "stop": 62149738}
        - {"contig": "chr9", "length": 499093, "start": 62249739, "stop": 62748832}
        - {"contig": "chr9", "length": 159538, "start": 62798833, "stop": 62958371}
        - {"contig": "chr9", "length": 194490, "start": 63008372, "stop": 63202862}
        - {"contig": "chr9", "length": 239401, "start": 63252863, "stop": 63492264}
        - {"contig": "chr9", "length": 376182, "start": 63542265, "stop": 63918447}
        - {"contig": "chr9", "length": 166565, "start": 63968448, "stop": 64135013}
        - {"contig": "chr9", "length": 30148, "start": 64185014, "stop": 64215162}
        - {"contig": "chr9", "length": 682961, "start": 64315163, "stop": 64998124}
        - {"contig": "chr9", "length": 31957, "start": 65048125, "stop": 65080082}
        - {"contig": "chr9", "length": 195040, "start": 65130083, "stop": 65325123}
        - {"contig": "chr9", "length": 220067, "start": 65375124, "stop": 65595191}
        - {"contig": "chr9", "length": 746195, "start": 65645192, "stop": 66391387}
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