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poruloh / Eagle

Haplotype phasing software
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Phasing cell line vcfs #38

Open aranham opened 1 year ago

aranham commented 1 year ago

I would like some guidance regarding an error that I get while running eagle2 for phasing. We have unphased vcf files for a cell line and we are using eagle2 to phase them. But I run into an error when I execute eagle2: "ERROR: target ploidy != 2 (ngt != 2*nsmpl): ngt=1, nsmpl=1"

Below is my run command: /.../Eagle_v2.4.1/eagle --numThreads 1 --vcfTarget /.../split.chr3.vcf.gz --vcfRef /.../1000G_hg38/chr3.genotypes.bcf --geneticMapFile=/.../Eagle_v2.4.1/tables/genetic_map_hg38_withX.txt.gz --outPrefix /.../split.chr3.vcf.gz.phased

Can you please provide us with some help on the error?

Thanks.

poruloh commented 1 year ago

It looks like some variants in your VCF are coded with a ploidy other than 2. I suggest checking that all genotypes are either 0/0, 0/1, or 1/1.

aranham commented 1 year ago

Thank you. That fixed the issue.