TOPMed imputed vcf to plink2 - dosage=DS or HDS

[Nicolas Rosewick]

Hello,

After imputation using TOPMed (Michigan server), and to convert vcf to plink2 format should I use dosage=DS or dosage=HDS in the plink2 command ?

plink2 --vcf imputed_chr1.vcf.gz dosage=DS --make-pgen --out imputed_chr1

or

plink2 --vcf imputed_chr1.vcf.gz dosage=HDS --make-pgen --out imputed_chr1

Thank you

[Christopher Chang]

HDS contains more information than DS.