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...") |
Johnbullard (talk | contribs) (Add links to 1.x versus 2.x documentation) |
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{|<!--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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--> | --> | ||
==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 | ||
| + | |||
| + | Version 2.x documentation: https://www.cog-genomics.org/plink/2.0/ | ||
|}} | |}} | ||
<!--PBS scripts--> | <!--PBS scripts--> | ||
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<!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | <!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | ||
__NOTOC____NOEDITSECTION__ | __NOTOC____NOEDITSECTION__ | ||
| + | =Validation= | ||
| + | * Validated 4/5/2018 | ||
Revision as of 15:30, 26 October 2021
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.
Required Modules
Serial
- plink
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/
Validation
- Validated 4/5/2018