How to imports DS field from VCF files with SeqArray seqVCF2GDS()
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ealopera • 0
@ealopera-14681
Last seen 24 months ago

Hello, I have VCF file coming from imputed data that contains three genotype info in three formats GT:DS:GP. Specifically, my dosage (DS) field is composed of CONTINUOUS values from 0 to 2. I use the function to convert this file to GDS. seqVCF2GDSfile.in, file.out,scenario="imputation")

and later I check the dosage field in the GDS with this command

seqGetData(genofile, "$dosage")

and I notice the dosage field contains only discrete values 0, 1 or 2, but not continuous. Which gives me the feeling that DS filed is not being imported but rather re-calculated. How can I change this?

seqArray seqVCF2GDS • 698 views
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@stephanie-m-gogarten-5121
Last seen 11 days ago
University of Washington

seqGetData(genofile, "$dosage") is indeed calculating dosage based on the "genotype" node. To read from the dosage node, you can use seqGetData(genofile, "annotation/format/DS"). Or you can use SeqVarTools::imputedDosage(), which does the same thing.

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