Question: Eagle error: Haploid genotype found
0
gravatar for myses030566
3 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 • 178 views
ADD COMMENTlink written 3 months ago by myses0305660

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

ADD REPLYlink written 3 months ago by Kevin Blighe33k

No. The VCF contains only chromosome 1-22 only

ADD REPLYlink written 3 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 3 months ago by Kevin Blighe33k

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

ADD REPLYlink written 3 months ago by Kevin Blighe33k
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