Genepop for LD testing SNPs dataset
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9 weeks ago

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 • 311 views
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How many SNP are we talking here ?

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Hi Nicolas,

I have a data set of 7698 SNPs to filter.

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

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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.