Entering edit mode
9.3 years ago
Dan
▴
540
The recommended SOP for recoding PED / MAP to VCF is:
plink --file <ped file name without extension> --recode vcf-iid --out <output file name without extension>
However, without specifying the reference sequence, how is the reference base in the VCF guessed?
Does plink have an extra option for passing the reference sequence when calling --recode
?
I'm reading about the associated file formats here:
- http://pngu.mgh.harvard.edu/~purcell/plink2/formats.html#map
- http://pngu.mgh.harvard.edu/~purcell/plink2/formats.html#fam
- http://pngu.mgh.harvard.edu/~purcell/plink2/formats.html#ped
and I don't see the reference base stored anywhere.