Dear all, Although this question may seem a bit trivial but can someone please explain what the GT field (0,1,2) imply in case of haploid organism.
I called SNP's using Haplotype caller. A typical entry is indicated below:
NW_001091929.1 14514 . T A 56.12 . AC=0;AF=0.00;AN=1;DP=1;FS=0.000;MQ=40.00;QD=28.06;SOR=2.303 GT:AD:DP:GQ:PL 0:1,0:1:41:0,41
I am aware that : 1) 0/0 - First allele is a reference base and second allele is a reference base (two alleles are present in two chromosomes)
2) 0/1 - First allele is a reference base and second allele is a alternate base (1 chr has ref base and its pair has alt base)
3) 1/1 - First allele is an alternate base and second allele is an alternate base (1 chr has alt base & its pair has alt base)
But since my organism is haploid and hence is N not 2N how do I interpret these values in that context and my GT field has value of 2 as well which is even more confusing.
Any help is deeply appreciated.