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How to compute DS (diploid dosage) from HDS (haploid dosage) in VCF? #2376

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NadiAlipour opened this issue Mar 5, 2025 · 0 comments
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@NadiAlipour
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NadiAlipour commented Mar 5, 2025

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.

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