Minnesota Supercomputing Institute
With regards to the safety measures put in place by the university to mitigate the risks of the COVID-19 virus, at this time all MSI systems will remain operational and can be accessed remotely as usual. The only planned outages concern our in-person Helpdesk and tutorials. More information, as well as alternative remote support options, can be found at MSI COVID-19 Continuity Plan
Tuesday, September 1, 2020
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.
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
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