what reads from original BAM are listed in mutect2 VCF-output?
Dear GATK team,
I am sorry if my question is naive. After running mutect2 (version 4.2) what positions (AND corresponding reads) from the original bam-file are reported in the vcf file? all that passed filters or only those that have the potential to be SNP/mutation?
I am analysing several cancer data sets in parallel and want to choose the most interesting for me SNPs. For this I want to know how many patients had WT at a particular positions, and how many had a possible mutation at this position. Can I find this information in the vcf file or do I need to refer to the original BAM?
For example, in the vcf file I have a postition chr1:111222 which is encountered in 8 patients with some AD values for normal and tumor samples. Does it mean that the original BAM file contain the same 8 patients at this position OR there may be more patients, but some of them are clearly wild-type and are not reported in vcf-file?
BTW, I am using vcf files (processed with mutect2) downloaded from the GDC data repository.
I hope for your help:)