Hello everyone,
For my analysis I am looking for a tool/method that makes from a list of selected SNPs (1000+) in the latest 1000 genomes data for all the SNPs that are in linkage disequilibrium (LD) with this SNP. There is already a tool for this SNAP tool ( http://www.broadinstitute.org/mpg/snap/ldsearch.php ) The SNAP tool is a very nice tool, but it only uses the 1000 genomes pilot so it is relatively old and now the LD blocks are much more split up in the latest 1000 genomes data if I check the 1000genomes web browser LD tool.
I found this analysis ( http://adairama.wordpress.com/2013/03/26/how-to-calculate-linkage-disequilibrium-using-vcf-of-the-latest-1000-genomes/ ) but it is genome wide and now already taking 25 days for chromosome 22 only and is not finished yet..
So does anyone knows how a similar tool/analysis like SNAP that uses the latest version of 1000 genomes?
Thanks!
See 1000 genomes LD calculation