How to compute DS (diploid dosage) from HDS (haploid dosage) in VCF?
1
0
Entering edit mode
3 months ago
Nadia • 0

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="Allele Probs for two haplotypes=Haploid Alternate Allele Dosage">

Thank you in advance for your guidance.

format question dosage hds • 419 views
ADD COMMENT
0
Entering edit mode

OK this is really a Minimac4 / Michigan Imputation Server concept, not a general VCF thing

ADD REPLY
0
Entering edit mode
3 months ago
LChart 5.0k

for biallelic sites, the trivial way is DS = HDS[0] + HDS[1]

ADD COMMENT

Login before adding your answer.

Traffic: 2140 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6