Difference between revisions of "Plink"

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(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|http://pngu.mgh.harvard.edu/~purcell/plink/}}
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|{{#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-->
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|{{#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_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory
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* 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==
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
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{{note|The API between 1.x and 2.x changed the command lines substantially}}
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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 15:30, 26 October 2021

Description

plink website  

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