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Convert Allele Dosage Files To Ped And Map

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

plink ped
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updated by zx8754 zx8754 • written by kapoor.manav • kapoor.manav

1 answer

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.

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written by zx8754 zx8754

Hi,

I am new to PLINK and GWAS studies. I am unsure how to write a script to convert my INFO/dosage file into a MAP file for an association study between genotype and 1 phenotype. So, first thing: I have an INFO file with information on the SNPs, the ID, position, allele 1 and 2 and Information on the imputation (see below)

rs148087467:60523:T:G 60523 T G 0.001 0.161 0.998 0 -1 -1 -1
--- 10:60684:A:C 60684 A C 0.029 0.713 0.978 0 -1 -1 -1

I want to create a script but have no idea how to convert this into a map file. I understand a MAP file has information on the chromosome code, variant identifier (rs), position/genetic distance (morgans) and base-pair co-ordinates (bp units).

Can someone please help me how to create a script! I am so new to all of this, so I do apologise.

Thank you!

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updated by zx8754 zx8754 • written by hkj7 • hkj7

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