I'm using samtools multisample SNP calling to call SNPs from different samples. The command I'm using is,
samtools mpileup -uf ref.fa *.bam | bcftools view -vcg - > out.vcf
Then, I'm using vcf-to-tab tool to convert vcf to tab file.
The problem is, No calls (missed in sequencing) are called as homozygous reference calls. How to differentiate No calls from homozygous reference calls.
I appreciate any sort of help.
Edit: My vcf file looks like this:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT samp1.bam samp2.bam 000000F 634700 . T C 3.55 . DP=1;AF1=1;AC1=4;DP4=0,0,0,1;MQ=60;FQ=-27.4 GT:PL:GQ 0/1:31,3,0:5 0/1:0,0,0:3