Difference between revisions of "Vcftools"
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| − | [[Category:Software]][[Category: | + | __NOTOC__ |
| − | {|<!-- | + | __NOEDITSECTION__ |
| + | [[Category:Software]][[Category:Biology]][[Category:Genomics]] | ||
| + | {|<!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|vcftools}} | |{{#vardefine:app|vcftools}} | ||
| − | |{{#vardefine:url| | + | |{{#vardefine:url|http://vcftools.sourceforge.net/}} |
| − | + | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | |
| − | |{{#vardefine: | + | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> |
| − | |{{#vardefine: | + | |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> |
| − | + | |{{#vardefine:policy|}} <!--Enable policy section --> | |
| − | |{{#vardefine: | + | |{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> |
| − | |{{#vardefine: | + | |{{#vardefine:faq|}} <!--Enable FAQ section --> |
| − | |{{#vardefine: | + | |{{#vardefine:citation|1}} <!--Enable Reference/Citation section --> |
| − | |{{#vardefine: | ||
| − | |{{#vardefine: | ||
|} | |} | ||
| − | <!-- | + | <!-- ######## 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 | + | 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. |
| − | + | [http://vcftools.sourceforge.net/docs.html Upstream documentation] for {{#var:app}}. | |
<!--Modules--> | <!--Modules--> | ||
==Environment Modules== | ==Environment Modules== | ||
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * | + | *HPC_VCFTOOLS_BIN - executable directory |
| − | + | {{#if: {{#var: exe}}|==How To Run== | |
| − | {{#if: {{#var: | + | 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: |
| − | |||
| − | |||
| − | < | ||
| − | |||
| − | + | mkdir -p tmp | |
| + | export TMPDIR="$(pwd)/tmp" | ||
| + | vcftools ... --temp ${TMPDIR} | ||
|}} | |}} | ||
| − | + | {{#if: {{#var: conf}}|==Configuration== | |
| − | {{#if: {{#var: | + | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} |
| − | See the [[{{PAGENAME}} | + | {{#if: {{#var: pbs}}|==PBS Script Examples== |
| − | |}} | + | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} |
| − | |||
{{#if: {{#var: policy}}|==Usage Policy== | {{#if: {{#var: policy}}|==Usage Policy== | ||
| − | + | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | |
| − | WRITE USAGE POLICY HERE ( | ||
| − | |||
| − | |}} | ||
| − | |||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
| − | + | WRITE PERFORMANCE TESTING RESULTS HERE|}} | |
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| − | |||
| − | |}} | ||
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{{#if: {{#var: faq}}|==FAQ== | {{#if: {{#var: faq}}|==FAQ== | ||
*'''Q:''' **'''A:'''|}} | *'''Q:''' **'''A:'''|}} | ||
| − | |||
{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
| − | If you publish research that uses | + | If you publish the research that uses this software please cite |
| − | + | <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. | |
| − | + | ||
| − | + | http://dx.doi.org/10.1093/bioinformatics/btr330 | |
| + | </code> | ||
|}} | |}} | ||
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Latest revision as of 20:55, 12 August 2022
Description
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.