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

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Nadia

• March 05, 2025 11:59

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 any way, 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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  Gökalp Çelik

  • March 07, 2025 08:25

  Hi Nadia

  If you are performing joint calling and imputation you may need to refer to the original imputation software for emitting those values since they are calculated based on the HMM performed in the algorithm. There may not be a simple solution to calculate those scores directly. Although we cannot provide any support you may wish to look at PLINK and PSEQ softwares for this purpose. 

  I hope this helps.

  Regards. 

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