Convert Allele Dosage Files To Ped And Map

Question

[kapoor.manav]

I have pedigree file in dosage format

FID IID PAT MAT SEX PHENOTYPE rs138257042_G rs141845380_C rs116378360_C a2x

100 001 016 017 2 2 NA NA NA 1

100 005 004 001 1 -9 2 2 1 1

100 008 007 006 1 1 2 2 2 2

and map file

22 rs138257042 0.027263 16449075 A G

22 rs141845380 0.027263 16449076 G A

22 rs116378360 0.027547 16620701 T C

22 a2x 0.027549 16620722 T C

I want to convert it to plink ped file. Please suggest some program or script to complete the task.

M

[zx8754]

Duplicate of this question? plink raw format to ped format

Answer 1

[zx8754]

rs138257042_G - G is the minor allele and the values 0,1,2 are the counts of minor allele. So, for IID=005 rs138257042 is G G. You can easily write up some code to do this kind of conversion.