Eagle error: Haploid genotype found
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?
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It could be that you have left chromosome Y variants in your file. Can you check?
No. The VCF contains only chromosome 1-22 only
Nomalise your file with
bcftools norm -m-any, and then try again. If all else fails, literally look through your file and search for any likely errors. Otherwise, contact the program developers.The error is called at exactly line 748, here: https://github.com/poruloh/Eagle/blob/master/src/GenoData.cpp