Measure Tag Snps, R Package, Tools

Question

[Cirrus]

Dear all,

is there any tool, which I can run on my local computer or R package to measure r^2 (LD) and identify tag SNPs?

I found tagger from the Broad Institue, but this is a web service. I need a local tool. coz I have a lot of data sets.

Many thanks for any hinds.

Answer 1

[Larry_Parnell]

HaploView and HelixTree are what we routinely use to perform this. These are superior stand-alone tools for this work.

[Cirrus]

Thanks a lot, I will use Haploview!!

Answer 2

[zx8754]

PriorityPruner

http://prioritypruner.sourceforge.net/

PriorityPruner is a software program which can prune a list of SNPs that are in high linkage disequilibrium (LD) with other SNPs in the list, while preferentially keeping/selecting SNPs of higher priority (e.g., the most significant SNPs in a genome-wide association study).

Input:

1. A genotype dataset (e.g., PLINK format)
2. A table of SNPs annotated with p-values or other prioritization criteria

Output:

1. A table of SNPs with columns indicating if the SNP is selected and/or tagged by a selected SNP