Difference between revisions of "Plink"
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The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results. | The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results. | ||
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
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Latest revision as of 20:25, 12 August 2022
Description
PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.
Environment Modules
Run module spider plink to find out what environment modules are available for this application.
System Variables
- HPC_PLINK_DIR - installation directory
- HPC_PLINK_BIN - executable directory
Additional Information
Version 1.x documentation: https://zzz.bwh.harvard.edu/plink/reference.shtml#options
Version 2.x documentation: https://www.cog-genomics.org/plink/2.0/