How To Convert Hapmap Genotypes Data To Plink Ped&Map Format
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Entering edit mode
10.1 years ago
J.F.Jiang ▴ 860

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 • 9.0k views
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5
Entering edit mode
9.9 years ago
Hsmart ▴ 60

Hi,

You can use Glu software http://code.google.com/p/glu-genetics/

With following command

glu transform HapMap_input -o Ped_output.ped -f hapmap

Best

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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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