ERROR: Non-diploid VCF entry detected. Each VCF entry must have a diploid genotype (GT) field consisting of two
alleles in the set {0,1,2} separated by either '/' or '|'. For example, "1/1", "0/1", and "0|2" are valid diploid
genotypes for HapCUT2, but "1", "0/3", and "0/0/1" are not.
The invalid entry is:
chr1 1396190 . GAA G,GA,GAAA 22.10 PASS . GT:GQ:DP:AD:VAF:PL 1/3:2:34:7,5,4,9:0.147059,0.117647,0.264706:16,1,37,2,34,34,2,0,2,29
Would it be possible to instead of raising an error here, just skipping these invalid variants. Maybe just output a warning instead. Since I would need to go back and filter out this variant its a bit annoying for the program to stop here.
I run into this error when running extractHairs
Would it be possible to instead of raising an error here, just skipping these invalid variants. Maybe just output a warning instead. Since I would need to go back and filter out this variant its a bit annoying for the program to stop here.