How to compute DS (diploid dosage) from HDS (haploid dosage) in VCF?

Open NadiAlipour opened this issue 10 months ago • 1 comments

Hello, I have a VCF file with GT:HDS (haploid dosage) values, but I need to generate GT:DS (diploid dosage), since this is the most common format in vcf files and used commonly for association analyses.

Is there a bcftools command or plugin to compute or convert the GT:DS field from GT:HDS?

The VCF FORMAT column is GT:HDS. A sample line looks like: chr22 10510303 ... GT:HDS 0|0:0,0 0|0:0.001,0 ...

VCF Header Snippet: ##FORMAT=<ID=HDS,Number=2,Type=Float,Description="Haploid Alternate Allele Dosage">

Thank you in advance for your guidance.

Mar 05 '25 10:03 NadiAlipour

Short answer is no, we don't have a plugin designed to do that. Possibly +fill-tags could be used for that. Can you explain how are the DS vs HDS values defined?

Mar 09 '25 15:03 pd3