ANGSD

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 package is built using SPACK and optimized for AVX, AVX2 and AVX512 CPUs. To use the optimized version, you need to add source /etc/profile.d/zlmod.sh to your submit script before loading any modules. By default, the AVX2 optimized version (head node is Haswell CPU) is in your path. The AVX2 optimized version will run on Skylake (enge, im2080, chem, health) and Cascade Lake (hawkcpu, hawkmem, hawkgpu, infolab) CPUs but not on Ivybridge (debug) CPUs.

Version	module	Notes
0.933	angsd/0.933

Example: /share/Apps/examples/angsd

#!/bin/bash

#SBATCH -p lts
#SBATCH -t 60
#SBATCH -n 1
#SBATCH -N 1

echo "This examples downloads sample data if not present"

if [[ ! -d bams ]]; then
  if [[ ! -f bams.tar.gz ]]; then
    wget http://popgen.dk/software/download/angsd/bams.tar.gz
    tar -xvzf bams.tar.gz
  fi
  module load samtools/1.10
  for i in bams/*.bam
  do
    samtools index $i
  done
  ls bams/*.bam > bam.filelist
  module unload samtools/1.10
fi

module load angsd

angsd -b bam.filelist -GL 1 -doMajorMinor 1 -doMaf 2 -P 5

angsd -b bam.filelist -GL 1 -doMajorMinor 1 -doMaf 2 -P 5 -minMapQ 30 -minQ 20 -minMaf 0.05

For more information visit http://www.popgen.dk/angsd/index.php/ANGSD