Hi,

I am variantcalling my 96 multi sampled bam file with samtools/bcftools however I obtain some strange results.

When I use the following command:

bcftools mpileup -O v -f ref.fa -a DP,AD,ADF,ADR,SP --threads 12 multi_sample_bam_file.bam | bcftools call -c -A -v -V indels --threads 12 -O z -o vcf_out.vcf.gz

I get for example, the following line:

Contig0 231901  .       C       T       999     .       DP=1725;VDB=0;SGB=556.637;RPB=0.87714;MQB=0.990852;BQB=0.0121288;MQ0F=0;AF1=0.540145;G3=0.451283,7.53222e-07,0.548716;HWE=4.30362e-25;AC1=104;DP4=829,0,764,0;MQ=60;FQ=999;PV4=1,1,0.0506106,1  GT:PL:DP:SP:ADF:ADR:AD  0/1:0,0,0:0:0:0,0:0,0:0,0    0/0:0,36,193:12:0:12,0:0,0:12,0 0/0:0,21,155:7:0:7,0:0,0:7,0    1/1:167,21,0:7:0:0,7:0,0:0,7

What I find kinda strange is that it shows this FORMAT: 1/0:0,0,0:0:0:0,0:0,0:0,0 Meaning it assigned a heterozygous genotype to my sample. However this sample has not a single read aligned. So shouldn't this be something like ./.:0,0,0:0:0:0,0:0,0:0,0 (No genotype called)

So my question is:

1. Why does this happen?
2. And is there and easy fix to set those genotypes to the correct ./. no call format?