Genepop for LD testing SNPs dataset

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3.5 years ago

giulia.trauzzi ▴ 30

Hello everyone,

I have a SNP data set to test for Linkage disequilibrium across all loci and I am running the command line in Genepop. I cannot use Plink to test for LD as my SNPs are not mapped (they were generated via a de novo approach). According to my calculations, the job would almost 3000 days to complete... (obviously not ideal). Is there a way I can calculate linkage disequilibrium on a large data set of SNPs? is there a way to speed up the process?

Thanks

Giulia

linkage genepop SNPs • 1.5k views

ADD COMMENT • link updated 3.5 years ago by Nicolas Rosewick 11k • written 3.5 years ago by giulia.trauzzi ▴ 30

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How many SNP are we talking here ?

ADD REPLY • link 3.5 years ago by Nicolas Rosewick 11k

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Hi Nicolas,

thanks for your reply.

I have a data set of 7698 SNPs to filter.

ADD REPLY • link 3.5 years ago by giulia.trauzzi ▴ 30

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Do not add answers unless you're answering the top level question. Use Add Comment/Add Reply instead as appropriate.

ADD REPLY • link 3.5 years ago by Ram 44k

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That is not a lot of SNP. What is the format of your data ? Maybe you can convert them into a plink (ped/map) format and use it to perform LD analysis.

ADD REPLY • link 3.5 years ago by Nicolas Rosewick 11k

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