Question: Eagle error: Haploid genotype found
0
gravatar for myses030566
23 months ago by
myses0305660 wrote:

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?

snp imputation next-gen gwas • 616 views
ADD COMMENTlink written 23 months ago by myses0305660

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

ADD REPLYlink written 23 months ago by Kevin Blighe61k

No. The VCF contains only chromosome 1-22 only

ADD REPLYlink written 23 months ago by myses0305660

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 REPLYlink written 23 months ago by Kevin Blighe61k

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

ADD REPLYlink written 23 months ago by Kevin Blighe61k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 840 users visited in the last hour