Question: GT (genotype information) in haploid organism has a value of 2 .
0
gravatar for shubhra.bhattacharya
20 months ago by
shubhra.bhattacharya120 wrote:

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.

snp genotype • 666 views
ADD COMMENTlink modified 18 months ago by Biostar ♦♦ 20 • written 20 months ago by shubhra.bhattacharya120
1

What version of GATK are you using? Did you specify the ploidy of your organism while running the analysis?

ADD REPLYlink written 18 months ago by Russ460

Yes I specified the ploidy as haploid.

ADD REPLYlink written 16 months ago by shubhra.bhattacharya120
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