Difference between revisions of "ANGSD"

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==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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Additional software included in this module:
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
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*contamination 
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*contamination2 
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*emOptim2 
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*msToGlf 
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*NGSadmix 
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*printIcounts 
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*realSFS 
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*smartCount 
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*splitgl 
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*supersim 
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*thetaStat
  
 
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If you publish research that uses {{#var:app}} you have to cite it as follows:
 
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[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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Latest revision as of 21:02, 6 December 2019

Description

angsd website  

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.

Required Modules

Serial

  • angsd

System Variables

  • HPC_ANGSD_DIR - installation directory

Additional Information

Additional software included in this module:

  • contamination
  • contamination2
  • emOptim2
  • msToGlf
  • NGSadmix
  • printIcounts
  • realSFS
  • smartCount
  • splitgl
  • supersim
  • thetaStat



Citation

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

Korneliussen et al. ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinformatics 2014, 15:356. doi:10.1186/s12859-014-0356-4.