Hi, I have variant calling pipeline for somatic mutations. I am trying to uncover mutations on low allele balance frequencies.
When I find mutation in particular sample, I would like to see if it is present in other samples. Unfortunately just comparing vcf files does not do the trick because of many possible filtering steps or lack of some calls. Thus for given signature of the mutation from vcf file I would like to obtain info regarding this particular mutation in number of bam files. In particular I am interested the most what is the coverage at the position of the mutation and what is the number of reads supporting the mutation.
For example I have 1.bam, 2.bam, 3.bam. Based on particular criteria (allele balance > 0.1, coverage > 500, allele observations > 10) i produce 1.vcf, 2.vcf, 3.vcf. Now when there is some variant in 1.bam based on these criteria, then in 2.bam there can be this mutation with allele balance 0.09, coverage 1000 and 9 allele observations (and it does not make it to 2.vcf) while in 3.bam there is 0 coverage and no allele observation. I would like to somehow extract this info about signatures of the mutations in 1.vcf in files 2.bam and 3.bam. What tool should I use and is there one?