In case this may be of help

[GuidoLeoni]

          In case this may be of help

the log file tells me that almost all the somatic variants were removed because not in het in the panel of normal .

INFO [2023-10-24 08:55:04] Loading coverage files...
INFO [2023-10-24 08:55:08] Mean target coverages: 240X (tumor) 235X (normal).
INFO [2023-10-24 08:55:10] Mean coverages: chrX: 113.73, chrY: 120.12, chr1-22: 228.96.
INFO [2023-10-24 08:55:11] Mean coverages: chrX: 121.64, chrY: 120.12, chr1-22: 227.41.
INFO [2023-10-24 08:55:26] Removing 3516 intervals with missing log.ratio.
INFO [2023-10-24 08:55:26] Removing 21 low/high GC targets.
INFO [2023-10-24 08:55:27] Removing 6377 intervals excluded in normalDB.
INFO [2023-10-24 08:55:27] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2023-10-24 08:55:27] Removing 61 low count (< 100 total reads) intervals.
INFO [2023-10-24 08:55:27] Removing 8523 low coverage (< 0.0015X) intervals.
WARN [2023-10-24 08:55:27] Low number of off-target intervals. You might want to exclude them (209557 on-target, 21660 off-target, ratio 0.09).
INFO [2023-10-24 08:55:27] Using 231217 intervals (209557 on-target, 21660 off-target).
INFO [2023-10-24 08:55:27] Ratio of mean on-target vs. off-target read counts: 0.19
INFO [2023-10-24 08:55:27] Mean off-target bin size: 96126
INFO [2023-10-24 08:55:29] AT/GC dropout: 1.03 (tumor), 1.01 (normal), 1.01 (coverage log-ratio).
INFO [2023-10-24 08:55:29] Loading VCF...
INFO [2023-10-24 08:57:03] Found 3115993 variants in VCF file.
INFO [2023-10-24 08:57:09] Removing 69933 triallelic sites.
WARN [2023-10-24 08:57:11] Found GERMQ info field with Phred scaled germline probabilities.
INFO [2023-10-24 08:57:20] Maximum of POPAP INFO is > 1, assuming -log10 scaled values
WARN [2023-10-24 08:57:25] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2023-10-24 08:57:29] 1951294 (64.1%) variants annotated as likely germline (DB INFO flag).
WARN [2023-10-24 08:58:37] Found 590496 variants with missing allelic fraction starting with chr1:10439_AC/A. Removing them.
INFO [2023-10-24 08:59:06] TUMOR is tumor in VCF file.
INFO [2023-10-24 08:59:22] 1792 homozygous and 1547 heterozygous variants on chrX.
INFO [2023-10-24 08:59:22] Sex from VCF: NA (Fisher's p-value: < 0.0001, odds-ratio: 3.63).
INFO [2023-10-24 08:59:22] Detected MuTect2 VCF.
INFO [2023-10-24 08:59:37] Removing 0 Mutect2 calls due to blacklisted failure reasons.
INFO [2023-10-24 08:59:42] Removing 2053349 non heterozygous (in matched normal) germline SNPs.
INFO [2023-10-24 08:59:42] Base quality scores range from -1 to 37 (offset by 1)
INFO [2023-10-24 08:59:43] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS.
INFO [2023-10-24 09:01:09] Initial testing for significant sample cross-contamination: unlikely
INFO [2023-10-24 09:01:11] Removing 209124 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15.
INFO [2023-10-24 09:01:11] Total size of targeted genomic region: 34.90Mb (53.62Mb with 50bp padding).
INFO [2023-10-24 09:01:14] 11.1% of targets contain variants.
INFO [2023-10-24 09:01:14] Removing 166082 variants outside intervals.
INFO [2023-10-24 09:01:14] Found SOMATIC annotation in VCF.

Originally posted by @GuidoLeoni in #329 (comment)