haploview

Module Name

haploview

Last Updated On

11/28/2023

Support Level

Secondary Support

Software Access Level

Open Access

Home Page

http://www.broad.mit.edu/mpg/haploview/index.php

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 isub command line:

isub -m 6gb
module load haploview
haploview

To run haploview with more memory (in megabytes) use the -memory option:

haploview -memory 2000

Haploview may report out-of-memory errors when working with large datasets on cl or blr nodes. Try logging out and reconnecting using isub until you are connected to a lab node, where Haploview runs without a problem. For additional information

http://www.broad.mit.edu/mpg/haploview/index.php{style="outline: 0px;" target="blank"}

Default

4.1

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4.1

Default

4.1

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Default

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