Difference between revisions of "ANGSD"

Latest revision as of 12:42, 12 August 2022

Description

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.

Environment Modules

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

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.

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
+[[Category:Software]][[Category:Biology]][[Category:NGS]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|angsd}}
@@ Line 22: / Line 22: @@
 <!--Modules-->
-==Required Modules==
+==Environment Modules==
-===Serial===
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-* {{#var:app}}
-<!--
-===Parallel (OpenMP)===
-* intel
-* {{#var:app}}
-===Parallel (MPI)===
-* intel
-* openmpi
-* {{#var:app}}
--->
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 42: / Line 32: @@
 <!--Run-->
 {{#if: {{#var: exe}}|==Additional Information==
-Utilities included in this module:
+Additional software included in this module:
-*angsd
 *contamination
 *contamination2