ANGSD

ANGSD can calculate various summary statistics, and perform association mapping and population genetic analyses utilising the full information in next generation sequencing data.

ANGSD is available as a module on Apocrita.

Usage

To run the default installed version of ANGSD, simply load the angsd module:

$ module load angsd
$ angsd
    -> angsd version: 0.919 (htslib: 1.5) build(Jul  4 2017 15:08:56)
    -> Please use the website "http://www.popgen.dk/angsd" as reference
    -> Use -nThreads or -P for number of threads allocated to the program
Overview of methods:
    -GL     Estimate genotype likelihoods
    -doCounts   Calculate various counts statistics
    -doAsso     Perform association study
    -doMaf      Estimate allele frequencies
...

Example job

Serial job

Here is an example job running with 2 cores and 10GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_rt=1:0:0
#$ -l h_vmem=5G

module load angsd

angsd -out outFile \
      -bam bam.list \
      -GL 1 \
      -doMaf 1 \
      -doMajorMinor 1 \
      -nThreads ${NSLOTS}

In this example, allele frequencies are estimated from genotype likelihoods with bam files as input using 2 threads.

References

• ANGSD GitHub
• ANGSD article