Difference between revisions of "SHAPEIT"

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(Created page with "Category:SoftwareCategory:BiologyCategory:SNP {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|shapeit}} |{{#vardefine:url|https://mathgen.stats.ox.ac.uk/genetic...")
 
 
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[[Category:Software]][[Category:Biology]][[Category:SNP]]
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[[Category:Software]][[Category:Biology]][[Category:Variant Calling]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|shapeit}}
 
|{{#vardefine:app|shapeit}}
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<!--Modules-->
 
<!--Modules-->
==Required Modules==
+
==Environment Modules==
 
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
 
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==

Latest revision as of 12:56, 15 August 2022

Description

shapeit website  

SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.

Environment Modules

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

System Variables

  • HPC_SHAPEIT_DIR - installation directory




Citation

If you publish research that uses shapeit you have to cite it as follows:

https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#citations