haploview
Summary
Module Name: haploview
Support Level: Secondary Support
Software Access Level: Open Access
Software Description
Haploview is a graphical program for haplotype analysis. It can analyze thousands of SNPs (tens of thousands in command line mode) in thousands of individuals. It supports the following functionalities: LD haplotype block analysis- haplotype population frequency estimation- single SNP and haplotype association tests- permutation testing for association significance- implementation of Paul de Bakker’s Tagger tag SNP selection algorithm- automatic download of phased genotype data from HapMap visualization and plotting of PLINK whole genome association results including advanced filtering options.
General Linux
Haploview requires a large amount of memory so it is recommended that you request more memory through the srun command line:
srun --pty --mem=6G bash
module load haploview
haploview
To run haploview with more memory (in megabytes) use the -memory option:
haploview -memory 2000
For additional information: