Eagle error: Haploid genotype found

0

Entering edit mode

5.7 years ago

myses030566 • 0

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?

imputation gwas SNP next-gen • 1.7k views

ADD COMMENT • link 5.7 years ago by myses030566 • 0

0

Entering edit mode

It could be that you have left chromosome Y variants in your file. Can you check?

ADD REPLY • link 5.7 years ago by Kevin Blighe 87k

0

Entering edit mode

No. The VCF contains only chromosome 1-22 only

ADD REPLY • link 5.7 years ago by myses030566 • 0

0

Entering edit mode

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.

ADD REPLY • link 5.7 years ago by Kevin Blighe 87k

0

Entering edit mode

The error is called at exactly line 748, here: https://github.com/poruloh/Eagle/blob/master/src/GenoData.cpp

ADD REPLY • link 5.7 years ago by Kevin Blighe 87k

Login before adding your answer.