I am trying to covert .ped and .map files to a VCF file using plink2, as in the examples below:
plink2 --ped test.ped --map .test.map --recode vcf --out testVCF
plink2 --file test --recode vcf --out testVCF
However, I am thrown the errors:
Error: Unrecognized flag ('--ped').
Error: Unrecognized flag ('--file').
Can anyone explain why this is?
I have been able to do the conversion using plink, however the REF alleles are incorrectly assigned (as is a well documented issue), and I do not have access to a reference file for the ~400K markers to define the reference alleles. I believe that plink2 is meant to have addressed this issue, and should correctly assign REF alleles.
Thanks in advance for any insight.