Hi. I am getting an error from EAGLE saying that I have a haploid genotype in my VCF.
ERROR: Haploid genotype found
So, I used the bcftools setGT plugin to convert any haploid genotype to "0|0":
bcftools +setGT file.vcf -- -t . -n 0p
But when I run the above command, the output shows:
Filled 0 alleles
which means there were no haploid genotypes in the first place. Anybody have any idea why EAGLE is throwing the error message?