Plink supports converting a VCF file to plink with the GT replaced with the DS value (–export vcf-dosage=DS ) The DS value ,dosage. is generated using TopMed imputation server and is perferred over GT for analysis. Could an option to export the DS be added to the HAIL plink_export method?
I don’t understand, from their documentation, this option seems to be for converting to VCF from PLINK2.
From plink2’s --export help.
* 'vcf', : VCF (default version 4.3). If PAR1 and PAR2 are present,
'vcf-4.2', they are automatically merged with chrX, with proper
'bcf', handling of chromosome codes and male ploidy.
'bcf-4.2' When the 'bgz' modifier is present, the VCF file is
block-gzipped. (This always happens with BCF output.)
The 'id-paste' modifier controls which .psam columns are
used to construct sample IDs (choices are maybefid, fid,
iid, maybesid, and sid; default is maybefid,iid,maybesid),
while the 'id-delim' modifier sets the character between the
ID pieces (default '_').
Genotypes are always exported. If you want to export a
sites-only VCF instead, see --make-pgen/--make-just-pvar's
'vcfheader' column set.
Dosages are not exported unless the 'vcf-dosage=' modifier
is present. The following six dosage export modes are
supported:
'GP': genotype posterior probabilities (v4.3 only).
'DS': Minimac3-style dosages, omitted for hardcalls.
'DS-force': Minimac3-style dosages, never omit.
'DS-only': Same as DS-force, except GT field is omitted.
'HDS': Minimac3-style phased dosages, omitted for hardcalls
and unphased calls. Also includes 'DS' output.
'HDS-force': Always report DS and HDS.