View source for ANGSD

[[Category:Software]][[Category:Biology]][[Category:NGS]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|angsd}}
|{{#vardefine:url|http://popgen.dk/wiki/index.php/ANGSD}}
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|{{#vardefine:conf|}}           <!--CONFIGURATION-->
|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
|{{#vardefine:policy|}}         <!--POLICY-->
|{{#vardefine:testing|}}       <!--PROFILING-->
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|{{#vardefine:citation|1}}       <!--CITATION-->
|{{#vardefine:installation|}} <!--INSTALLATION-->
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<!--Description-->
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

ANGSD is a software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium depth data. The software is written in C++ and has been used on large sample sizes.
This program is not for manipulating '.bam' files, but solely a tool to perform various kinds of analysis. We recommend the excellent program SAMtools for outputting and modifying bamfiles.

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==Environment Modules==
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
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{{#if: {{#var: exe}}|==Additional Information==
Additional software included in this module:
*contamination  
*contamination2  
*emOptim2  
*msToGlf  
*NGSadmix  
*printIcounts  
*realSFS  
*smartCount  
*splitgl  
*supersim  
*thetaStat

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{{#if: {{#var: pbs}}|==PBS Script Examples==
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.
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<!--Policy-->
{{#if: {{#var: policy}}|==Usage Policy==

WRITE USAGE POLICY HERE (Licensing, usage, access).

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{{#if: {{#var: testing}}|==Performance==

WRITE_PERFORMANCE_TESTING_RESULTS_HERE

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<!--Faq-->
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
<!--Citation-->
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{#var:app}} you have to cite it as follows:

[http://www.biomedcentral.com/1471-2105/15/356/abstract Korneliussen et al.] ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinformatics 2014, 15:356.  doi:10.1186/s12859-014-0356-4.

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{{#if: {{#var: installation}}|==Installation==
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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