I am using GATK UnifiedGenotyper 2.3-9 for a set of pooled samples. I am uncertain about the order of PL values in polyploid samples, as it wasn't defined in VCF v4.1 specifications. The ordering formula described in VCF v4.1: F(j/k) = (k*(k+1)/2)+j only applies to diploid case. May I know how GATK extended the ordering formula to handle polypoid samples?
Example VCF line: GT:AD:DP:GQ:MLPSAC:MLPSAF:PL 0/0/1/1/1/1/1/1:71,177:249:17:6:0.750:5685,995,510,254,101,17,0,92,32767
Thank you very much!
Best regards, Allen
Hello, I have 454 reads of loci on polyploid individuals. I am able to produce assemblies containing the different copies of one locus per individual. But I want to extract the reads corresponding to each copies, to then be able to produce phylogenies. Does the GATK can do something like this?