Difference between revisions of "Plink"
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Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:BioinformaticsCategory:PhylogeneticsCategory:Genomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|plink}} |{{#vardefine:url|ht...") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]][[Category:Genomics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|plink}} | |{{#vardefine:app|plink}} | ||
| − | |{{#vardefine:url| | + | |{{#vardefine:url|https://zzz.bwh.harvard.edu/plink/}} |
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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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. | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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| − | < | ||
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{# | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | {{note|The API between 1.x and 2.x changed the command lines substantially}} | |
| + | Version 1.x documentation: https://zzz.bwh.harvard.edu/plink/reference.shtml#options | ||
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| + | Version 2.x documentation: https://www.cog-genomics.org/plink/2.0/ | ||
|}} | |}} | ||
<!--PBS scripts--> | <!--PBS scripts--> | ||
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
The API between 1.x and 2.x changed the command lines substantially
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/