How To Convert Hapmap Genotypes Data To Plink Ped&Map Format
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11.2 years ago
J.F.Jiang ▴ 880

hello, everyone!

recently, I want to do some study on LD relationship of SNPs on whole-genome scale.

i am told that one can use hapmap LD data offerred via hapmap or can use some softwares to simulate.

i: i download the latest LD data and use some data from a publised paper for comparison but found differently not the same.

so i asked the author which data they used and which method they handled. The author told me that the hapmap II+III rel27 b36 version data were get from hapmap which i had download it again, and the software is plink.

while i took some time to look at the software and i realize the different input file format must be convert into.

So, i came across the problem how can i use the original fwd.txt to obtain the plink ped and map file?

ps: although the hapmap offerred us hapmap phase3 r2 plink data, but i just want to learn that how can i handle this problem!

hope that who can give me the answer or softwares or scipts!

and at last, i want to know if there are any significant difference between hapmap data and 1000Gonome project data for LD calculation?

linkage hapmap plink • 9.5k views
Entering edit mode
11.1 years ago
Hsmart ▴ 60


You can use Glu software

With following command

glu transform HapMap_input -o Ped_output.ped -f hapmap


Entering edit mode

Hi Hsmart,

Could you break that command down for me? I'm not really sure how that fits in with the example in the documentation glu transform samples.ldat --includesamples=controls -o controls.sdat where you seem to tell glu what to turn into what purely from the file endings?


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