REQUIRED for all errors and issues:
a) GATK version used: v184.108.40.206
b) Exact command used: see below
c) Entire program log: see below
I want to ask whether Mutect2 can call tumor sample-specific mutations under multi-sample mode. For example, I have three biopsy samples taken from a patient with cancer: two from the tumors (PAAD11M and PAAD11T) and the other from a matched normal tissue (PAAD11N). And then I called mutations using Mutect2 as follows:
gatk --java-options '-Xmx5g' Mutect2 \
-R /data/reference/gatk_resource/Homo_sapiens_assembly38.fasta \
--intervals /data/reference/WES/S07604514_Regions.bed \
--interval-padding 100 -I /data/xieduo/Immun_genomics/data/Łuksza_2022_Nature/bam/PAAD11M.bam \
-I /data/xieduo/Immun_genomics/data/Łuksza_2022_Nature/bam/PAAD11T.bam \
-I /data/xieduo/Immun_genomics/data/Łuksza_2022_Nature/bam/PAAD11N.bam \
-normal PAAD11N --germline-resource /data/reference/gatk_resource/af-only-gnomad.hg38.vcf.gz
After that, I checked the PAAD11_somatic.snv.vcf file and try to find tumor sample-specific mutation (for example, the GT of a mutation in PAAD11T is 0/0 but is 0/1 in PAAD11M). However, I couldn't find any mutation that fits this pattern. Is this caused by the joint calling of multi-sample mode (the 8th point in https://gatk.broadinstitute.org/hc/en-us/articles/360050722212-FAQ-for-Mutect2)?
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