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.
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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 |
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| 0.933 | angsd/0.933 |
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#!/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/2019-11-05
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