Making Linkage Disequilibrium blocks from SNPs position for NCBI Build 38 ?

Bahar Sedaghati-khayat @Bahar-Sedaghati-Khayat

05 July 2016 1 7K Report

Hello evryone

I'd like to know if anyone has or might know how can I make LD block from my SNPs list for the last human genome build (GRCh38). I'm currently working on the GWAS Iranian population. I'm trying remove high LD regions from my dataset in QC prosses.

I using of plink r2 command for finding connected SNPs. but I can't find the best way for estimating region LD blocks!

anyone can help me

Thanks a lot in advance for the attention!

Knut M. Wittkowski

36 is still the most recent build with LD available, but there is at least a tool to "remap" the 36 LD blocks to the 38 positions (or the 38 positions to the 36 positions):

http://www.ncbi.nlm.nih.gov/genome/tools/remap

I hope this helps.

Knut

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