Mixed haploid and diploid genotypes in the release VCF from the Diversity Panel

Open JRodrigoF opened this issue 5 years ago • 1 comments

Hi,

To report the presence of both haploid and diploid genotypes in the output from GVCF Genotyper Version: 2.1.0. The file is merged.vcf.gz dowloaded from BaseSpace.

Since these are human data, all called genotypes should have two alleles. Am I missing something here sorry?

Jun 12 '20 00:06 JRodrigoF

Hi, thanks for your interest in Polaris and GVCF Genotyper. The Human autosomes are mostly (!) diploid but for the other chromosomes, this isn't always the case. Could you share an example of a genotype that is causing you problems?

Jul 22 '20 09:07 olest