-
Notifications
You must be signed in to change notification settings - Fork 11
/
Copy pathvcf_header02.txt
757 lines (757 loc) · 59.2 KB
/
vcf_header02.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
##fileformat=VCFv4.2
##reference=file:///media/everestial007/SeagateBackup4.0TB/RNAseq_Data_Analyses/02_Alignment_To_Ref - New/GVCF_Calls_onGenes-RunningTest01/02-JointGenotyping_MySpF1/lyrata_genome.fa
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=my_indel_filter,Description="QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0">
##FILTER=<ID=my_snp_filter,Description="QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##GATKCommandLine.CombineVariants=<ID=CombineVariants,CommandLineOptions="analysis_type=CombineVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=lyrata_genome.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=HignConfSNPs source=HighConf_Variants.asPASSED.AllSamples.vcf)]), (RodBindingCollection [(RodBinding name=SNPs source=DNA_Samples.Passed.SNPs_allHetsRemoved.vcf)]), (RodBindingCollection [(RodBinding name=InDels source=DNA_Samples.Passed.InDels_allHetsRemoved.vcf)])] out=/media/everestial007/SeagateBackup4.0TB/RNAseq_Data_Analyses/02_Alignment_To_Ref - New/GVCF_Calls_onGenes-RunningTest01/02-JointGenotyping_MySpF1/DNA_Samples.Passed_Variants.vcf genotypemergeoption=UNSORTED filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED multipleallelesmergetype=BY_TYPE rod_priority_list=null printComplexMerges=false filteredAreUncalled=false minimalVCF=false excludeNonVariants=false setKey=set assumeIdenticalSamples=false minimumN=1 suppressCommandLineHeader=false mergeInfoWithMaxAC=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Thu Dec 21 23:56:42 EST 2017",Epoch=1513918602988,Version=3.7-0-gcfedb67>
##GATKCommandLine.GenotypeGVCFs=<ID=GenotypeGVCFs,CommandLineOptions="analysis_type=GenotypeGVCFs input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=lyrata_genome.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=MA605.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant2 source=MA611.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant3 source=MA622.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant4 source=MA625.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant5 source=MA629.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant6 source=Ncm8.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant7 source=Sp3.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant8 source=Sp21.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant9 source=Sp76.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant10 source=Sp154.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant11 source=Sp164.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant12 source=SpNor33.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant13 source=ms01e.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant14 source=ms02g.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant15 source=ms03g.raw.snps.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant16 source=ms04h.raw.snps.indels.g.vcf)])] out=/media/everestial007/SeagateBackup4.0TB/RNAseq_Data_Analyses/02_Alignment_To_Ref - New/GVCF_Calls_onGenes/raw_variants.AllSamples.MySpF1.vcf includeNonVariantSites=false uniquifySamples=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=10.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=2 annotation=[] group=[StandardAnnotation] dbsnp=(RodBinding name= source=UNBOUND) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Sat Dec 16 20:17:48 EST 2017",Epoch=1513473468011,Version=3.8-0-ge9d806836>
##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[good_Coverage.mapQ20.sorted.MA611.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[2:15881000-15902000, 3:12165000-12174000] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/home/bkgiri/apps/RefGenomeN_index/lyrata_genome.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[StandardAnnotation, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=FASTEST_AVAILABLE phredScaledGlobalReadMismappingRate=45 noFpga=false nativePairHmmThreads=1 useDoublePrecision=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxReadsInMemoryPerSample=30000 maxTotalReadsInMemory=10000000 maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Fri Dec 15 18:29:51 EST 2017",Epoch=1513380591593,Version=3.8-0-ge9d806836>
##GATKCommandLine.SelectVariants.2=<ID=SelectVariants,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=lyrata_genome.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=Remaining.Variants.AllSamples.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/media/everestial007/SeagateBackup4.0TB/RNAseq_Data_Analyses/02_Alignment_To_Ref - New/GVCF_Calls_onGenes-RunningTest01/02-JointGenotyping_MySpF1/DNA_Samples.raw_SNPs.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[ms01e, ms02g, ms03g, ms04h] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[vc.getCalledChrCount() == 0] invertselect=true excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=true restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Thu Dec 21 23:18:22 EST 2017",Epoch=1513916302870,Version=3.8-0-ge9d806836>
##GATKCommandLine.SelectVariants.3=<ID=SelectVariants,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=lyrata_genome.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=DNA_Samples.Filtered_SNPs.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/media/everestial007/SeagateBackup4.0TB/RNAseq_Data_Analyses/02_Alignment_To_Ref - New/GVCF_Calls_onGenes-RunningTest01/02-JointGenotyping_MySpF1/DNA_Samples.Passed_SNPs.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[vc.isNotFiltered()] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Thu Dec 21 23:20:01 EST 2017",Epoch=1513916401173,Version=3.7-0-gcfedb67>
##GATKCommandLine.SelectVariants.4=<ID=SelectVariants,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=lyrata_genome.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=DNA_Samples.Passed_SNPs.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/media/everestial007/SeagateBackup4.0TB/RNAseq_Data_Analyses/02_Alignment_To_Ref - New/GVCF_Calls_onGenes-RunningTest01/02-JointGenotyping_MySpF1/DNA_Samples.Passed.SNPs_allHetsRemoved.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[vc.getHetCount() == vc.getCalledChrCount()/2] invertselect=true excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Thu Dec 21 23:20:23 EST 2017",Epoch=1513916423031,Version=3.7-0-gcfedb67>
##GATKCommandLine.SelectVariants=<ID=SelectVariants,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=lyrata_genome.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=raw_variants.AllSamples.MySpF1.vcf) discordance=(RodBinding name=discordance source=Detlef.Variants.asPASSED.vcf) concordance=(RodBinding name= source=UNBOUND) out=/media/everestial007/SeagateBackup4.0TB/RNAseq_Data_Analyses/02_Alignment_To_Ref - New/GVCF_Calls_onGenes-RunningTest01/02-JointGenotyping_MySpF1/Remaining.Variants.AllSamples.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Thu Dec 21 23:10:31 EST 2017",Epoch=1513915831133,Version=3.8-0-ge9d806836>
##GATKCommandLine.VariantFiltration=<ID=VariantFiltration,CommandLineOptions="analysis_type=VariantFiltration input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=lyrata_genome.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=DNA_Samples.raw_SNPs.vcf) mask=(RodBinding name= source=UNBOUND) out=/media/everestial007/SeagateBackup4.0TB/RNAseq_Data_Analyses/02_Alignment_To_Ref - New/GVCF_Calls_onGenes-RunningTest01/02-JointGenotyping_MySpF1/DNA_Samples.Filtered_SNPs.vcf filterExpression=[QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0] filterName=[my_snp_filter] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask filterNotInMask=false missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false invertFilterExpression=false invertGenotypeFilterExpression=false setFilteredGtToNocall=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Thu Dec 21 23:19:58 EST 2017",Epoch=1513916398266,Version=3.7-0-gcfedb67>
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants">
##contig=<ID=scaffold_1118,length=1005>
##contig=<ID=scaffold_1117,length=1017>
##contig=<ID=scaffold_1116,length=1032>
##contig=<ID=scaffold_1113,length=1037>
##contig=<ID=scaffold_1112,length=1047>
##contig=<ID=scaffold_1111,length=1078>
##contig=<ID=scaffold_1109,length=1083>
##contig=<ID=scaffold_1106,length=1174>
##contig=<ID=scaffold_1105,length=1194>
##contig=<ID=scaffold_1102,length=1249>
##contig=<ID=scaffold_1099,length=1362>
##contig=<ID=scaffold_1096,length=1413>
##contig=<ID=scaffold_1095,length=1425>
##contig=<ID=scaffold_1094,length=1447>
##contig=<ID=scaffold_1091,length=1567>
##contig=<ID=scaffold_1090,length=1576>
##contig=<ID=scaffold_1089,length=1632>
##contig=<ID=scaffold_1086,length=1720>
##contig=<ID=scaffold_1084,length=1840>
##contig=<ID=scaffold_1080,length=1964>
##contig=<ID=scaffold_1044,length=2691>
##contig=<ID=scaffold_1021,length=3008>
##contig=<ID=scaffold_1034,length=3146>
##contig=<ID=scaffold_1072,length=3249>
##contig=<ID=scaffold_999,length=3250>
##contig=<ID=scaffold_1097,length=3259>
##contig=<ID=scaffold_1085,length=3303>
##contig=<ID=scaffold_1069,length=3355>
##contig=<ID=scaffold_1025,length=3368>
##contig=<ID=scaffold_1032,length=3379>
##contig=<ID=scaffold_1087,length=3400>
##contig=<ID=scaffold_1074,length=3416>
##contig=<ID=scaffold_983,length=3426>
##contig=<ID=scaffold_1082,length=3428>
##contig=<ID=scaffold_982,length=3429>
##contig=<ID=scaffold_998,length=3458>
##contig=<ID=scaffold_1017,length=3499>
##contig=<ID=scaffold_1012,length=3507>
##contig=<ID=scaffold_1056,length=3510>
##contig=<ID=scaffold_1057,length=3517>
##contig=<ID=scaffold_1070,length=3525>
##contig=<ID=scaffold_960,length=3538>
##contig=<ID=scaffold_975,length=3568>
##contig=<ID=scaffold_1064,length=3571>
##contig=<ID=scaffold_955,length=3571>
##contig=<ID=scaffold_954,length=3584>
##contig=<ID=scaffold_1058,length=3585>
##contig=<ID=scaffold_1078,length=3595>
##contig=<ID=scaffold_1041,length=3612>
##contig=<ID=scaffold_946,length=3616>
##contig=<ID=scaffold_945,length=3617>
##contig=<ID=scaffold_1043,length=3621>
##contig=<ID=scaffold_1054,length=3622>
##contig=<ID=scaffold_939,length=3631>
##contig=<ID=scaffold_993,length=3636>
##contig=<ID=scaffold_1052,length=3641>
##contig=<ID=scaffold_936,length=3647>
##contig=<ID=scaffold_991,length=3657>
##contig=<ID=scaffold_1033,length=3660>
##contig=<ID=scaffold_1022,length=3679>
##contig=<ID=scaffold_928,length=3697>
##contig=<ID=scaffold_924,length=3704>
##contig=<ID=scaffold_941,length=3726>
##contig=<ID=scaffold_919,length=3737>
##contig=<ID=scaffold_1040,length=3746>
##contig=<ID=scaffold_918,length=3747>
##contig=<ID=scaffold_915,length=3754>
##contig=<ID=scaffold_1029,length=3768>
##contig=<ID=scaffold_996,length=3769>
##contig=<ID=scaffold_912,length=3771>
##contig=<ID=scaffold_938,length=3779>
##contig=<ID=scaffold_1046,length=3782>
##contig=<ID=scaffold_965,length=3785>
##contig=<ID=scaffold_979,length=3792>
##contig=<ID=scaffold_1003,length=3794>
##contig=<ID=scaffold_1000,length=3807>
##contig=<ID=scaffold_896,length=3846>
##contig=<ID=scaffold_1061,length=3854>
##contig=<ID=scaffold_1010,length=3854>
##contig=<ID=scaffold_894,length=3855>
##contig=<ID=scaffold_1008,length=3858>
##contig=<ID=scaffold_1031,length=3861>
##contig=<ID=scaffold_1014,length=3862>
##contig=<ID=scaffold_893,length=3862>
##contig=<ID=scaffold_992,length=3872>
##contig=<ID=scaffold_1006,length=3877>
##contig=<ID=scaffold_1001,length=3881>
##contig=<ID=scaffold_964,length=3891>
##contig=<ID=scaffold_1007,length=3901>
##contig=<ID=scaffold_883,length=3909>
##contig=<ID=scaffold_881,length=3916>
##contig=<ID=scaffold_1020,length=3919>
##contig=<ID=scaffold_879,length=3924>
##contig=<ID=scaffold_1048,length=3927>
##contig=<ID=scaffold_1005,length=3927>
##contig=<ID=scaffold_878,length=3930>
##contig=<ID=scaffold_1015,length=3932>
##contig=<ID=scaffold_940,length=3938>
##contig=<ID=scaffold_875,length=3940>
##contig=<ID=scaffold_963,length=3949>
##contig=<ID=scaffold_984,length=3958>
##contig=<ID=scaffold_872,length=3968>
##contig=<ID=scaffold_891,length=4007>
##contig=<ID=scaffold_866,length=4016>
##contig=<ID=scaffold_880,length=4021>
##contig=<ID=scaffold_908,length=4028>
##contig=<ID=scaffold_968,length=4042>
##contig=<ID=scaffold_1019,length=4049>
##contig=<ID=scaffold_976,length=4054>
##contig=<ID=scaffold_989,length=4061>
##contig=<ID=scaffold_858,length=4066>
##contig=<ID=scaffold_971,length=4079>
##contig=<ID=scaffold_853,length=4089>
##contig=<ID=scaffold_852,length=4092>
##contig=<ID=scaffold_851,length=4097>
##contig=<ID=scaffold_911,length=4098>
##contig=<ID=scaffold_849,length=4099>
##contig=<ID=scaffold_848,length=4102>
##contig=<ID=scaffold_1053,length=4104>
##contig=<ID=scaffold_986,length=4114>
##contig=<ID=scaffold_920,length=4123>
##contig=<ID=scaffold_895,length=4136>
##contig=<ID=scaffold_861,length=4139>
##contig=<ID=scaffold_962,length=4142>
##contig=<ID=scaffold_900,length=4145>
##contig=<ID=scaffold_987,length=4148>
##contig=<ID=scaffold_970,length=4154>
##contig=<ID=scaffold_835,length=4174>
##contig=<ID=scaffold_834,length=4178>
##contig=<ID=scaffold_868,length=4182>
##contig=<ID=scaffold_832,length=4187>
##contig=<ID=scaffold_830,length=4194>
##contig=<ID=scaffold_981,length=4203>
##contig=<ID=scaffold_828,length=4207>
##contig=<ID=scaffold_958,length=4209>
##contig=<ID=scaffold_994,length=4210>
##contig=<ID=scaffold_977,length=4214>
##contig=<ID=scaffold_825,length=4247>
##contig=<ID=scaffold_890,length=4249>
##contig=<ID=scaffold_905,length=4260>
##contig=<ID=scaffold_978,length=4265>
##contig=<ID=scaffold_823,length=4267>
##contig=<ID=scaffold_887,length=4269>
##contig=<ID=scaffold_950,length=4273>
##contig=<ID=scaffold_843,length=4275>
##contig=<ID=scaffold_871,length=4285>
##contig=<ID=scaffold_817,length=4298>
##contig=<ID=scaffold_815,length=4310>
##contig=<ID=scaffold_1076,length=4311>
##contig=<ID=scaffold_882,length=4320>
##contig=<ID=scaffold_813,length=4331>
##contig=<ID=scaffold_937,length=4338>
##contig=<ID=scaffold_831,length=4344>
##contig=<ID=scaffold_829,length=4347>
##contig=<ID=scaffold_901,length=4359>
##contig=<ID=scaffold_877,length=4368>
##contig=<ID=scaffold_805,length=4370>
##contig=<ID=scaffold_804,length=4377>
##contig=<ID=scaffold_802,length=4396>
##contig=<ID=scaffold_903,length=4408>
##contig=<ID=scaffold_798,length=4415>
##contig=<ID=scaffold_797,length=4423>
##contig=<ID=scaffold_796,length=4429>
##contig=<ID=scaffold_884,length=4431>
##contig=<ID=scaffold_855,length=4439>
##contig=<ID=scaffold_793,length=4441>
##contig=<ID=scaffold_792,length=4443>
##contig=<ID=scaffold_788,length=4458>
##contig=<ID=scaffold_819,length=4465>
##contig=<ID=scaffold_784,length=4474>
##contig=<ID=scaffold_783,length=4478>
##contig=<ID=scaffold_865,length=4494>
##contig=<ID=scaffold_781,length=4495>
##contig=<ID=scaffold_990,length=4503>
##contig=<ID=scaffold_801,length=4509>
##contig=<ID=scaffold_845,length=4512>
##contig=<ID=scaffold_812,length=4514>
##contig=<ID=scaffold_864,length=4516>
##contig=<ID=scaffold_779,length=4521>
##contig=<ID=scaffold_838,length=4523>
##contig=<ID=scaffold_777,length=4536>
##contig=<ID=scaffold_814,length=4539>
##contig=<ID=scaffold_790,length=4554>
##contig=<ID=scaffold_811,length=4562>
##contig=<ID=scaffold_787,length=4568>
##contig=<ID=scaffold_773,length=4573>
##contig=<ID=scaffold_862,length=4575>
##contig=<ID=scaffold_772,length=4582>
##contig=<ID=scaffold_771,length=4584>
##contig=<ID=scaffold_782,length=4595>
##contig=<ID=scaffold_786,length=4606>
##contig=<ID=scaffold_766,length=4606>
##contig=<ID=scaffold_763,length=4616>
##contig=<ID=scaffold_762,length=4621>
##contig=<ID=scaffold_837,length=4626>
##contig=<ID=scaffold_759,length=4630>
##contig=<ID=scaffold_756,length=4643>
##contig=<ID=scaffold_755,length=4645>
##contig=<ID=scaffold_753,length=4660>
##contig=<ID=scaffold_752,length=4661>
##contig=<ID=scaffold_780,length=4662>
##contig=<ID=scaffold_747,length=4673>
##contig=<ID=scaffold_746,length=4685>
##contig=<ID=scaffold_769,length=4691>
##contig=<ID=scaffold_744,length=4703>
##contig=<ID=scaffold_741,length=4712>
##contig=<ID=scaffold_740,length=4713>
##contig=<ID=scaffold_739,length=4724>
##contig=<ID=scaffold_738,length=4726>
##contig=<ID=scaffold_736,length=4732>
##contig=<ID=scaffold_735,length=4737>
##contig=<ID=scaffold_734,length=4745>
##contig=<ID=scaffold_733,length=4746>
##contig=<ID=scaffold_729,length=4780>
##contig=<ID=scaffold_728,length=4797>
##contig=<ID=scaffold_727,length=4814>
##contig=<ID=scaffold_723,length=4825>
##contig=<ID=scaffold_721,length=4834>
##contig=<ID=scaffold_961,length=4838>
##contig=<ID=scaffold_716,length=4853>
##contig=<ID=scaffold_715,length=4861>
##contig=<ID=scaffold_713,length=4863>
##contig=<ID=scaffold_711,length=4872>
##contig=<ID=scaffold_710,length=4912>
##contig=<ID=scaffold_707,length=4917>
##contig=<ID=scaffold_702,length=4958>
##contig=<ID=scaffold_701,length=4959>
##contig=<ID=scaffold_776,length=4960>
##contig=<ID=scaffold_700,length=4965>
##contig=<ID=scaffold_697,length=4979>
##contig=<ID=scaffold_693,length=4983>
##contig=<ID=scaffold_902,length=5000>
##contig=<ID=scaffold_688,length=5023>
##contig=<ID=scaffold_686,length=5026>
##contig=<ID=scaffold_867,length=5049>
##contig=<ID=scaffold_761,length=5050>
##contig=<ID=scaffold_682,length=5054>
##contig=<ID=scaffold_679,length=5059>
##contig=<ID=scaffold_795,length=5066>
##contig=<ID=scaffold_699,length=5067>
##contig=<ID=scaffold_678,length=5083>
##contig=<ID=scaffold_904,length=5088>
##contig=<ID=scaffold_674,length=5112>
##contig=<ID=scaffold_694,length=5113>
##contig=<ID=scaffold_671,length=5118>
##contig=<ID=scaffold_670,length=5121>
##contig=<ID=scaffold_669,length=5128>
##contig=<ID=scaffold_668,length=5132>
##contig=<ID=scaffold_667,length=5140>
##contig=<ID=scaffold_683,length=5141>
##contig=<ID=scaffold_664,length=5148>
##contig=<ID=scaffold_663,length=5148>
##contig=<ID=scaffold_662,length=5156>
##contig=<ID=scaffold_661,length=5160>
##contig=<ID=scaffold_695,length=5175>
##contig=<ID=scaffold_658,length=5205>
##contig=<ID=scaffold_681,length=5213>
##contig=<ID=scaffold_655,length=5225>
##contig=<ID=scaffold_680,length=5240>
##contig=<ID=scaffold_666,length=5241>
##contig=<ID=scaffold_717,length=5243>
##contig=<ID=scaffold_653,length=5252>
##contig=<ID=scaffold_651,length=5261>
##contig=<ID=scaffold_731,length=5275>
##contig=<ID=scaffold_649,length=5283>
##contig=<ID=scaffold_719,length=5313>
##contig=<ID=scaffold_659,length=5359>
##contig=<ID=scaffold_705,length=5366>
##contig=<ID=scaffold_638,length=5368>
##contig=<ID=scaffold_636,length=5373>
##contig=<ID=scaffold_726,length=5424>
##contig=<ID=scaffold_631,length=5424>
##contig=<ID=scaffold_629,length=5457>
##contig=<ID=scaffold_628,length=5459>
##contig=<ID=scaffold_627,length=5482>
##contig=<ID=scaffold_626,length=5482>
##contig=<ID=scaffold_625,length=5482>
##contig=<ID=scaffold_672,length=5491>
##contig=<ID=scaffold_646,length=5493>
##contig=<ID=scaffold_685,length=5534>
##contig=<ID=scaffold_616,length=5563>
##contig=<ID=scaffold_615,length=5574>
##contig=<ID=scaffold_614,length=5576>
##contig=<ID=scaffold_630,length=5629>
##contig=<ID=scaffold_608,length=5644>
##contig=<ID=scaffold_810,length=5651>
##contig=<ID=scaffold_748,length=5666>
##contig=<ID=scaffold_604,length=5673>
##contig=<ID=scaffold_603,length=5688>
##contig=<ID=scaffold_591,length=5806>
##contig=<ID=scaffold_639,length=5820>
##contig=<ID=scaffold_665,length=5827>
##contig=<ID=scaffold_840,length=5829>
##contig=<ID=scaffold_637,length=5829>
##contig=<ID=scaffold_684,length=5838>
##contig=<ID=scaffold_589,length=5841>
##contig=<ID=scaffold_587,length=5857>
##contig=<ID=scaffold_677,length=5864>
##contig=<ID=scaffold_584,length=5890>
##contig=<ID=scaffold_582,length=5927>
##contig=<ID=scaffold_580,length=5936>
##contig=<ID=scaffold_579,length=5937>
##contig=<ID=scaffold_575,length=5959>
##contig=<ID=scaffold_573,length=5973>
##contig=<ID=scaffold_569,length=5983>
##contig=<ID=scaffold_565,length=6009>
##contig=<ID=scaffold_562,length=6014>
##contig=<ID=scaffold_642,length=6019>
##contig=<ID=scaffold_597,length=6031>
##contig=<ID=scaffold_594,length=6032>
##contig=<ID=scaffold_947,length=6058>
##contig=<ID=scaffold_557,length=6061>
##contig=<ID=scaffold_552,length=6083>
##contig=<ID=scaffold_564,length=6109>
##contig=<ID=scaffold_602,length=6162>
##contig=<ID=scaffold_592,length=6190>
##contig=<ID=scaffold_576,length=6219>
##contig=<ID=scaffold_770,length=6232>
##contig=<ID=scaffold_532,length=6269>
##contig=<ID=scaffold_554,length=6283>
##contig=<ID=scaffold_704,length=6290>
##contig=<ID=scaffold_612,length=6294>
##contig=<ID=scaffold_610,length=6315>
##contig=<ID=scaffold_525,length=6326>
##contig=<ID=scaffold_520,length=6360>
##contig=<ID=scaffold_519,length=6361>
##contig=<ID=scaffold_531,length=6372>
##contig=<ID=scaffold_516,length=6382>
##contig=<ID=scaffold_512,length=6411>
##contig=<ID=scaffold_645,length=6504>
##contig=<ID=scaffold_507,length=6505>
##contig=<ID=scaffold_617,length=6537>
##contig=<ID=scaffold_607,length=6542>
##contig=<ID=scaffold_510,length=6553>
##contig=<ID=scaffold_501,length=6594>
##contig=<ID=scaffold_500,length=6608>
##contig=<ID=scaffold_496,length=6643>
##contig=<ID=scaffold_585,length=6689>
##contig=<ID=scaffold_595,length=6717>
##contig=<ID=scaffold_558,length=6765>
##contig=<ID=scaffold_491,length=6784>
##contig=<ID=scaffold_486,length=6821>
##contig=<ID=scaffold_675,length=6837>
##contig=<ID=scaffold_635,length=6847>
##contig=<ID=scaffold_807,length=6854>
##contig=<ID=scaffold_481,length=6892>
##contig=<ID=scaffold_509,length=6900>
##contig=<ID=scaffold_706,length=7009>
##contig=<ID=scaffold_469,length=7057>
##contig=<ID=scaffold_549,length=7074>
##contig=<ID=scaffold_468,length=7083>
##contig=<ID=scaffold_488,length=7089>
##contig=<ID=scaffold_480,length=7093>
##contig=<ID=scaffold_487,length=7116>
##contig=<ID=scaffold_535,length=7120>
##contig=<ID=scaffold_485,length=7120>
##contig=<ID=scaffold_463,length=7147>
##contig=<ID=scaffold_540,length=7151>
##contig=<ID=scaffold_470,length=7167>
##contig=<ID=scaffold_461,length=7174>
##contig=<ID=scaffold_482,length=7203>
##contig=<ID=scaffold_472,length=7204>
##contig=<ID=scaffold_493,length=7252>
##contig=<ID=scaffold_505,length=7365>
##contig=<ID=scaffold_475,length=7365>
##contig=<ID=scaffold_551,length=7366>
##contig=<ID=scaffold_504,length=7398>
##contig=<ID=scaffold_460,length=7398>
##contig=<ID=scaffold_449,length=7416>
##contig=<ID=scaffold_489,length=7466>
##contig=<ID=scaffold_447,length=7466>
##contig=<ID=scaffold_446,length=7466>
##contig=<ID=scaffold_492,length=7480>
##contig=<ID=scaffold_451,length=7539>
##contig=<ID=scaffold_527,length=7565>
##contig=<ID=scaffold_443,length=7567>
##contig=<ID=scaffold_467,length=7598>
##contig=<ID=scaffold_439,length=7615>
##contig=<ID=scaffold_588,length=7625>
##contig=<ID=scaffold_462,length=7632>
##contig=<ID=scaffold_435,length=7656>
##contig=<ID=scaffold_429,length=7683>
##contig=<ID=scaffold_453,length=7712>
##contig=<ID=scaffold_428,length=7726>
##contig=<ID=scaffold_427,length=7728>
##contig=<ID=scaffold_436,length=7748>
##contig=<ID=scaffold_433,length=7762>
##contig=<ID=scaffold_484,length=7775>
##contig=<ID=scaffold_548,length=7813>
##contig=<ID=scaffold_457,length=7818>
##contig=<ID=scaffold_471,length=7831>
##contig=<ID=scaffold_426,length=7840>
##contig=<ID=scaffold_474,length=7843>
##contig=<ID=scaffold_413,length=8084>
##contig=<ID=scaffold_416,length=8111>
##contig=<ID=scaffold_450,length=8167>
##contig=<ID=scaffold_455,length=8208>
##contig=<ID=scaffold_412,length=8224>
##contig=<ID=scaffold_464,length=8265>
##contig=<ID=scaffold_415,length=8283>
##contig=<ID=scaffold_477,length=8359>
##contig=<ID=scaffold_403,length=8363>
##contig=<ID=scaffold_419,length=8366>
##contig=<ID=scaffold_401,length=8402>
##contig=<ID=scaffold_431,length=8404>
##contig=<ID=scaffold_398,length=8508>
##contig=<ID=scaffold_397,length=8535>
##contig=<ID=scaffold_408,length=8592>
##contig=<ID=scaffold_441,length=8626>
##contig=<ID=scaffold_390,length=8733>
##contig=<ID=scaffold_396,length=8738>
##contig=<ID=scaffold_384,length=8774>
##contig=<ID=scaffold_383,length=8774>
##contig=<ID=scaffold_381,length=8802>
##contig=<ID=scaffold_380,length=8802>
##contig=<ID=scaffold_379,length=8803>
##contig=<ID=scaffold_378,length=8822>
##contig=<ID=scaffold_375,length=8855>
##contig=<ID=scaffold_386,length=8868>
##contig=<ID=scaffold_385,length=8873>
##contig=<ID=scaffold_566,length=8876>
##contig=<ID=scaffold_372,length=8876>
##contig=<ID=scaffold_624,length=8921>
##contig=<ID=scaffold_402,length=8929>
##contig=<ID=scaffold_409,length=8939>
##contig=<ID=scaffold_366,length=8942>
##contig=<ID=scaffold_365,length=8943>
##contig=<ID=scaffold_368,length=9003>
##contig=<ID=scaffold_361,length=9014>
##contig=<ID=scaffold_371,length=9041>
##contig=<ID=scaffold_358,length=9041>
##contig=<ID=scaffold_363,length=9090>
##contig=<ID=scaffold_355,length=9149>
##contig=<ID=scaffold_354,length=9157>
##contig=<ID=scaffold_352,length=9205>
##contig=<ID=scaffold_350,length=9246>
##contig=<ID=scaffold_349,length=9250>
##contig=<ID=scaffold_348,length=9251>
##contig=<ID=scaffold_346,length=9256>
##contig=<ID=scaffold_376,length=9273>
##contig=<ID=scaffold_344,length=9289>
##contig=<ID=scaffold_343,length=9298>
##contig=<ID=scaffold_340,length=9319>
##contig=<ID=scaffold_339,length=9323>
##contig=<ID=scaffold_337,length=9326>
##contig=<ID=scaffold_335,length=9336>
##contig=<ID=scaffold_351,length=9344>
##contig=<ID=scaffold_334,length=9371>
##contig=<ID=scaffold_341,length=9405>
##contig=<ID=scaffold_332,length=9416>
##contig=<ID=scaffold_330,length=9444>
##contig=<ID=scaffold_342,length=9505>
##contig=<ID=scaffold_400,length=9516>
##contig=<ID=scaffold_364,length=9531>
##contig=<ID=scaffold_325,length=9588>
##contig=<ID=scaffold_322,length=9656>
##contig=<ID=scaffold_320,length=9724>
##contig=<ID=scaffold_319,length=9767>
##contig=<ID=scaffold_388,length=9797>
##contig=<ID=scaffold_310,length=9954>
##contig=<ID=scaffold_307,length=10021>
##contig=<ID=scaffold_357,length=10030>
##contig=<ID=scaffold_304,length=10091>
##contig=<ID=scaffold_303,length=10106>
##contig=<ID=scaffold_327,length=10118>
##contig=<ID=scaffold_345,length=10120>
##contig=<ID=scaffold_300,length=10133>
##contig=<ID=scaffold_305,length=10182>
##contig=<ID=scaffold_298,length=10202>
##contig=<ID=scaffold_302,length=10227>
##contig=<ID=scaffold_293,length=10266>
##contig=<ID=scaffold_299,length=10268>
##contig=<ID=scaffold_292,length=10276>
##contig=<ID=scaffold_295,length=10362>
##contig=<ID=scaffold_294,length=10363>
##contig=<ID=scaffold_285,length=10478>
##contig=<ID=scaffold_284,length=10500>
##contig=<ID=scaffold_287,length=10534>
##contig=<ID=scaffold_283,length=10573>
##contig=<ID=scaffold_290,length=10597>
##contig=<ID=scaffold_281,length=10755>
##contig=<ID=scaffold_315,length=10914>
##contig=<ID=scaffold_288,length=10982>
##contig=<ID=scaffold_417,length=11063>
##contig=<ID=scaffold_311,length=11111>
##contig=<ID=scaffold_268,length=11135>
##contig=<ID=scaffold_277,length=11163>
##contig=<ID=scaffold_266,length=11173>
##contig=<ID=scaffold_265,length=11173>
##contig=<ID=scaffold_269,length=11233>
##contig=<ID=scaffold_262,length=11236>
##contig=<ID=scaffold_267,length=11253>
##contig=<ID=scaffold_261,length=11263>
##contig=<ID=scaffold_347,length=11265>
##contig=<ID=scaffold_264,length=11275>
##contig=<ID=scaffold_286,length=11290>
##contig=<ID=scaffold_275,length=11334>
##contig=<ID=scaffold_258,length=11345>
##contig=<ID=scaffold_279,length=11393>
##contig=<ID=scaffold_251,length=11483>
##contig=<ID=scaffold_271,length=11518>
##contig=<ID=scaffold_289,length=11519>
##contig=<ID=scaffold_270,length=11521>
##contig=<ID=scaffold_249,length=11536>
##contig=<ID=scaffold_248,length=11543>
##contig=<ID=scaffold_253,length=11547>
##contig=<ID=scaffold_252,length=11573>
##contig=<ID=scaffold_259,length=11642>
##contig=<ID=scaffold_250,length=11642>
##contig=<ID=scaffold_247,length=11656>
##contig=<ID=scaffold_278,length=11661>
##contig=<ID=scaffold_246,length=11661>
##contig=<ID=scaffold_241,length=11720>
##contig=<ID=scaffold_240,length=11761>
##contig=<ID=scaffold_239,length=11778>
##contig=<ID=scaffold_243,length=11791>
##contig=<ID=scaffold_374,length=11842>
##contig=<ID=scaffold_244,length=11945>
##contig=<ID=scaffold_233,length=11955>
##contig=<ID=scaffold_236,length=11975>
##contig=<ID=scaffold_231,length=12023>
##contig=<ID=scaffold_255,length=12066>
##contig=<ID=scaffold_228,length=12137>
##contig=<ID=scaffold_230,length=12195>
##contig=<ID=scaffold_223,length=12436>
##contig=<ID=scaffold_221,length=12465>
##contig=<ID=scaffold_242,length=12482>
##contig=<ID=scaffold_219,length=12503>
##contig=<ID=scaffold_220,length=12567>
##contig=<ID=scaffold_213,length=12589>
##contig=<ID=scaffold_212,length=12623>
##contig=<ID=scaffold_216,length=12667>
##contig=<ID=scaffold_215,length=12671>
##contig=<ID=scaffold_208,length=12734>
##contig=<ID=scaffold_207,length=12741>
##contig=<ID=scaffold_235,length=12746>
##contig=<ID=scaffold_206,length=12758>
##contig=<ID=scaffold_225,length=12774>
##contig=<ID=scaffold_210,length=12820>
##contig=<ID=scaffold_214,length=12939>
##contig=<ID=scaffold_203,length=12995>
##contig=<ID=scaffold_205,length=13037>
##contig=<ID=scaffold_234,length=13216>
##contig=<ID=scaffold_323,length=13369>
##contig=<ID=scaffold_211,length=13490>
##contig=<ID=scaffold_197,length=13548>
##contig=<ID=scaffold_209,length=13614>
##contig=<ID=scaffold_301,length=13661>
##contig=<ID=scaffold_193,length=13678>
##contig=<ID=scaffold_188,length=14062>
##contig=<ID=scaffold_189,length=14063>
##contig=<ID=scaffold_229,length=14132>
##contig=<ID=scaffold_201,length=14150>
##contig=<ID=scaffold_226,length=14339>
##contig=<ID=scaffold_181,length=14397>
##contig=<ID=scaffold_199,length=14456>
##contig=<ID=scaffold_195,length=14542>
##contig=<ID=scaffold_179,length=14583>
##contig=<ID=scaffold_190,length=14608>
##contig=<ID=scaffold_191,length=14737>
##contig=<ID=scaffold_177,length=14777>
##contig=<ID=scaffold_196,length=14784>
##contig=<ID=scaffold_176,length=14793>
##contig=<ID=scaffold_180,length=14826>
##contig=<ID=scaffold_184,length=14860>
##contig=<ID=scaffold_222,length=14935>
##contig=<ID=scaffold_172,length=15141>
##contig=<ID=scaffold_173,length=15208>
##contig=<ID=scaffold_170,length=15673>
##contig=<ID=scaffold_165,length=15836>
##contig=<ID=scaffold_164,length=15851>
##contig=<ID=scaffold_178,length=15941>
##contig=<ID=scaffold_163,length=15971>
##contig=<ID=scaffold_166,length=16014>
##contig=<ID=scaffold_158,length=16071>
##contig=<ID=scaffold_159,length=16148>
##contig=<ID=scaffold_160,length=16358>
##contig=<ID=scaffold_169,length=16599>
##contig=<ID=scaffold_149,length=16847>
##contig=<ID=scaffold_151,length=17353>
##contig=<ID=scaffold_143,length=17394>
##contig=<ID=scaffold_141,length=17526>
##contig=<ID=scaffold_142,length=17620>
##contig=<ID=scaffold_139,length=17624>
##contig=<ID=scaffold_138,length=17628>
##contig=<ID=scaffold_161,length=17702>
##contig=<ID=scaffold_146,length=17905>
##contig=<ID=scaffold_137,length=18049>
##contig=<ID=scaffold_136,length=18177>
##contig=<ID=scaffold_132,length=18203>
##contig=<ID=scaffold_129,length=18393>
##contig=<ID=scaffold_125,length=18511>
##contig=<ID=scaffold_121,length=18658>
##contig=<ID=scaffold_122,length=18722>
##contig=<ID=scaffold_130,length=18728>
##contig=<ID=scaffold_128,length=18776>
##contig=<ID=scaffold_133,length=18967>
##contig=<ID=scaffold_126,length=19147>
##contig=<ID=scaffold_135,length=19286>
##contig=<ID=scaffold_120,length=19368>
##contig=<ID=scaffold_115,length=19382>
##contig=<ID=scaffold_152,length=19386>
##contig=<ID=scaffold_114,length=19422>
##contig=<ID=scaffold_113,length=19435>
##contig=<ID=scaffold_112,length=19564>
##contig=<ID=scaffold_123,length=19715>
##contig=<ID=scaffold_118,length=19913>
##contig=<ID=scaffold_106,length=20070>
##contig=<ID=scaffold_103,length=20430>
##contig=<ID=scaffold_108,length=20787>
##contig=<ID=scaffold_110,length=20827>
##contig=<ID=scaffold_100,length=20959>
##contig=<ID=scaffold_98,length=20962>
##contig=<ID=scaffold_99,length=21256>
##contig=<ID=scaffold_96,length=21493>
##contig=<ID=scaffold_117,length=21951>
##contig=<ID=scaffold_91,length=22377>
##contig=<ID=scaffold_90,length=22400>
##contig=<ID=scaffold_97,length=22403>
##contig=<ID=scaffold_89,length=22846>
##contig=<ID=scaffold_85,length=24006>
##contig=<ID=scaffold_88,length=24147>
##contig=<ID=scaffold_83,length=24864>
##contig=<ID=scaffold_76,length=26132>
##contig=<ID=scaffold_73,length=26592>
##contig=<ID=scaffold_77,length=26910>
##contig=<ID=scaffold_72,length=27939>
##contig=<ID=scaffold_71,length=28414>
##contig=<ID=scaffold_66,length=28436>
##contig=<ID=scaffold_74,length=30081>
##contig=<ID=scaffold_63,length=30383>
##contig=<ID=scaffold_70,length=30586>
##contig=<ID=scaffold_57,length=35077>
##contig=<ID=scaffold_61,length=37089>
##contig=<ID=scaffold_387,length=38674>
##contig=<ID=scaffold_92,length=41166>
##contig=<ID=scaffold_185,length=41385>
##contig=<ID=scaffold_144,length=42461>
##contig=<ID=scaffold_53,length=42563>
##contig=<ID=scaffold_68,length=42762>
##contig=<ID=scaffold_109,length=42950>
##contig=<ID=scaffold_80,length=44312>
##contig=<ID=scaffold_86,length=47099>
##contig=<ID=scaffold_84,length=47761>
##contig=<ID=scaffold_65,length=48666>
##contig=<ID=scaffold_167,length=49487>
##contig=<ID=scaffold_47,length=50189>
##contig=<ID=scaffold_87,length=50767>
##contig=<ID=scaffold_37,length=50885>
##contig=<ID=scaffold_64,length=51199>
##contig=<ID=scaffold_38,length=54598>
##contig=<ID=scaffold_60,length=54680>
##contig=<ID=scaffold_36,length=55443>
##contig=<ID=scaffold_39,length=56741>
##contig=<ID=scaffold_52,length=57915>
##contig=<ID=scaffold_58,length=58233>
##contig=<ID=scaffold_43,length=58977>
##contig=<ID=scaffold_54,length=59709>
##contig=<ID=scaffold_59,length=60404>
##contig=<ID=scaffold_51,length=60900>
##contig=<ID=scaffold_32,length=67898>
##contig=<ID=scaffold_24,length=72324>
##contig=<ID=scaffold_25,length=76307>
##contig=<ID=scaffold_22,length=77967>
##contig=<ID=scaffold_29,length=77981>
##contig=<ID=scaffold_27,length=79363>
##contig=<ID=scaffold_48,length=82330>
##contig=<ID=scaffold_28,length=82702>
##contig=<ID=scaffold_34,length=82892>
##contig=<ID=scaffold_41,length=83393>
##contig=<ID=scaffold_35,length=85588>
##contig=<ID=scaffold_23,length=95112>
##contig=<ID=scaffold_20,length=100232>
##contig=<ID=scaffold_31,length=104288>
##contig=<ID=scaffold_33,length=127197>
##contig=<ID=scaffold_19,length=129820>
##contig=<ID=scaffold_21,length=154816>
##contig=<ID=scaffold_18,length=163736>
##contig=<ID=scaffold_16,length=170080>
##contig=<ID=scaffold_17,length=170241>
##contig=<ID=scaffold_26,length=171326>
##contig=<ID=scaffold_15,length=269926>
##contig=<ID=scaffold_13,length=274490>
##contig=<ID=scaffold_14,length=361337>
##contig=<ID=scaffold_11,length=440609>
##contig=<ID=scaffold_10,length=461865>
##contig=<ID=scaffold_9,length=1906741>
##contig=<ID=2,length=19320864>
##contig=<ID=5,length=21221946>
##contig=<ID=8,length=22951293>
##contig=<ID=4,length=23328337>
##contig=<ID=3,length=24464547>
##contig=<ID=7,length=24649197>
##contig=<ID=6,length=25113588>
##contig=<ID=1,length=33132539>
##reference=file:///media/everestial007/SeagateBackup4.0TB/RNAseq_Data_Analyses/02_Alignment_To_Ref - New/GVCF_Calls_onGenes-RunningTest01/02-JointGenotyping_MySpF1/lyrata_genome.fa
##source=SelectVariants
##FORMAT=<ID=PG,Number=1,Type=String,Description="phASER Local Genotype">
##FORMAT=<ID=PB,Number=1,Type=String,Description="phASER Local Block">
##FORMAT=<ID=PI,Number=1,Type=String,Description="phASER Local Block Index (unique for each block)">
##FORMAT=<ID=PM,Number=1,Type=String,Description="phASER Local Block Maximum Variant MAF">
##FORMAT=<ID=PW,Number=1,Type=String,Description="phASER Genome Wide Genotype">
##FORMAT=<ID=PC,Number=1,Type=String,Description="phASER Genome Wide Confidence">
##source_20180106.1=vcf-merge(r953) ms01e_phased_updated.vcf.gz ms02g_phased_updated.vcf.gz ms03g_phased_updated.vcf.gz ms04h_phased_updated.vcf.gz MA611_phased_updated.vcf.gz MA605_phased_updated.vcf.gz MA622_phased_updated.vcf.gz
##sourceFiles_20180106.1=0:ms01e_phased_updated.vcf.gz,1:ms02g_phased_updated.vcf.gz,2:ms03g_phased_updated.vcf.gz,3:ms04h_phased_updated.vcf.gz,4:MA611_phased_updated.vcf.gz,5:MA605_phased_updated.vcf.gz,6:MA622_phased_updated.vcf.gz
##INFO=<ID=SF,Number=.,Type=String,Description="Source File (index to sourceFiles, f when filtered)">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive)
##GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive)
##GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive)
##GVCFBlock58-59=minGQ=58(inclusive),maxGQ=59(exclusive)
##INFO=<ID=TS,Type=Test,Description="Allele count in genotypes">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ms01e ms02g ms03g ms04h MA611 MA605 MA622