I'm using Samtools and BCFtools v0.1.19 for variant calling and read that the genotype field is unreliable for bcftools
I am running it in paired mode, here is an example command:
samtools mpileup -C50 -RDSBuf <reference.fasta> <tumor.bam> <normal.bam> | bcftools view -vcgINT pair - > out
One line for example:
10 5321495 . C A 54 . DP=133;VDB=1.121900e-01;RPB=-3.926675e-03;AF1=0.25;CLR=87;AC1=1;DP4=59,62,1,11;MQ=49;FQ=55.2;PV4=0.012,1,9.4e-32,1 GT:PL:DP:SP:GQ 0/0:0,130,255:123:24:99 0/1:87,0,243:10:0:85
Tells me that the tumor.bam does not have the alternate allele while the normal.bam is heterozygous for the allele. When I investigate it in IGV I see that the alternate allele does exist in the tumor, it just isn't reflected by the genotype in the VCF for whatever reason. What factors can cause this behaviour and how can I reliably tell if a mutation is absent, heterozygous, or homozygous?