Difference between revisions of "Vcftools"

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[[Category:Software]][[Category:biology]][[Category:bioinformatics]][[Category:genomics]]
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__NOTOC__
{|<!--CONFIGURATION: REQUIRED-->
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__NOEDITSECTION__
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[[Category:Software]][[Category:Biology]][[Category:Genomics]]
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{|<!--Main settings - REQUIRED-->
 
|{{#vardefine:app|vcftools}}
 
|{{#vardefine:app|vcftools}}
|{{#vardefine:url|https://vcftools.github.io/index.html}}
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|{{#vardefine:url|http://vcftools.sourceforge.net/}}
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
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|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
|{{#vardefine:conf|}}           <!--CONFIGURATION-->
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|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
|{{#vardefine:exe|}}           <!--ADDITIONAL INFO-->
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|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
|{{#vardefine:job|}}           <!--JOB SCRIPTS-->
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|{{#vardefine:policy|}} <!--Enable policy section -->
|{{#vardefine:policy|}}         <!--POLICY-->
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|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
|{{#vardefine:testing|}}       <!--PROFILING-->
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|{{#vardefine:faq|}} <!--Enable FAQ section -->
|{{#vardefine:faq|}}             <!--FAQ-->
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|{{#vardefine:citation|1}} <!--Enable Reference/Citation section -->
|{{#vardefine:citation|}}       <!--CITATION-->
 
|{{#vardefine:installation|}} <!--INSTALLATION-->
 
 
|}
 
|}
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<!-- ########  Template Body ######## -->
 
<!--Description-->
 
<!--Description-->
 
{{#if: {{#var: url}}|
 
{{#if: {{#var: url}}|
 
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
  
VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
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VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide methods for working with VCF files: validating, merging, comparing and calculate some basic population genetic statistics.  
 
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[http://vcftools.sourceforge.net/docs.html Upstream documentation] for {{#var:app}}.
 
<!--Modules-->
 
<!--Modules-->
 
==Environment Modules==
 
==Environment Modules==
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==System Variables==
 
==System Variables==
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
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*HPC_VCFTOOLS_BIN - executable directory
<!--Configuration-->
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{{#if: {{#var: exe}}|==How To Run==
{{#if: {{#var: conf}}|==Configuration==
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By default vcftools uses /tmp for temporary file storage. As explained in [https://vcftools.github.io/man_latest.html vcftools documentation] you should use the <code>--temp</code> argument to point vcftools to a directory in your /blue space instead since HiPerGator2 nodes are diskless and the /tmp directory on them is very small. For example, the following can be used in a job script:
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
 
|}}
 
<!--Run-->
 
{{#if: {{#var: exe}}|==Additional Information==
 
  
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
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mkdir -p tmp
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export TMPDIR="$(pwd)/tmp"
  
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vcftools ... --temp ${TMPDIR}
 
|}}
 
|}}
<!--Job Scripts-->
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{{#if: {{#var: conf}}|==Configuration==
{{#if: {{#var: job}}|==Job Script Examples==
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See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.
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{{#if: {{#var: pbs}}|==PBS Script Examples==
|}}
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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
<!--Policy-->
 
 
{{#if: {{#var: policy}}|==Usage Policy==
 
{{#if: {{#var: policy}}|==Usage Policy==
 
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WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
WRITE USAGE POLICY HERE (Licensing, usage, access).
 
 
 
|}}
 
<!--Performance-->
 
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==
 
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WRITE PERFORMANCE TESTING RESULTS HERE|}}
WRITE_PERFORMANCE_TESTING_RESULTS_HERE
 
 
 
|}}
 
<!--Faq-->
 
 
{{#if: {{#var: faq}}|==FAQ==
 
{{#if: {{#var: faq}}|==FAQ==
 
*'''Q:''' **'''A:'''|}}
 
*'''Q:''' **'''A:'''|}}
<!--Citation-->
 
 
{{#if: {{#var: citation}}|==Citation==
 
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{#var:app}} you have to cite it as follows:
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If you publish the research that uses this software please cite
 
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<code>The Variant Call Format and VCFtools, Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter, Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin and 1000 Genomes Project Analysis Group, Bioinformatics, 2011.
WRITE_CITATION_HERE
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http://dx.doi.org/10.1093/bioinformatics/btr330
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</code>
 
|}}
 
|}}
<!--Installation-->
 
{{#if: {{#var: installation}}|==Installation==
 
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
 
__NOTOC____NOEDITSECTION__
 

Latest revision as of 20:55, 12 August 2022

Description

vcftools website  

VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide methods for working with VCF files: validating, merging, comparing and calculate some basic population genetic statistics. Upstream documentation for vcftools.

Environment Modules

Run module spider vcftools to find out what environment modules are available for this application.

System Variables

  • HPC_VCFTOOLS_DIR - installation directory
  • HPC_VCFTOOLS_BIN - executable directory

How To Run

By default vcftools uses /tmp for temporary file storage. As explained in vcftools documentation you should use the --temp argument to point vcftools to a directory in your /blue space instead since HiPerGator2 nodes are diskless and the /tmp directory on them is very small. For example, the following can be used in a job script:

mkdir -p tmp
export TMPDIR="$(pwd)/tmp"
vcftools ... --temp ${TMPDIR}



Citation

If you publish the research that uses this software please cite The Variant Call Format and VCFtools, Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter, Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin and 1000 Genomes Project Analysis Group, Bioinformatics, 2011.

http://dx.doi.org/10.1093/bioinformatics/btr330