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.
What version of GATK are you using? Did you specify the ploidy of your organism while running the analysis?
Yes I specified the ploidy as haploid.