This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Genepop for LD testing SNPs dataset

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
• 2,312 views • link
updated by Nicolas Rosewick Nicolas Rosewick • written by giulia.trauzzi • giulia.trauzzi

Hi Nicolas,

thanks for your reply.

I have a data set of 7698 SNPs to filter.

• 0 views • link
written by giulia.trauzzi • giulia.trauzzi

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

• 0 views • link
written by Ram Ram

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.

• 0 views • link
written by Nicolas Rosewick Nicolas Rosewick

0 answers

No answers yet.

Log in to answer this question.

More posts like this