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Overview

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/CRAM files, but solely a tool to perform various kinds of analysis. We recommend the excellent program SAMtools for outputting and modifying bamfile

Using

Use the module name angsd to discover versions available and to load the application.

Example

[]$ angsd --help
	-> angsd version: 0.935 (htslib: 1.12) build(Jun 15 2021 09:02:30)
	-> angsd --help 
	-> angsd version: 0.935 (htslib: 1.12) build(Jun 15 2021 09:02:31)
	-> 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
	-doError	Estimate the type specific error rates
	-doAncError	Estimate the errorrate based on perfect fastas
	-HWE_pval	Est inbreedning per site or use as filter
	-doGeno		Call genotypes
	-doFasta	Generate a fasta for a BAM file
	-doAbbababa	Perform an ABBA-BABA test
	-sites		Analyse specific sites (can force major/minor)
	-doSaf		Estimate the SFS and/or neutrality tests genotype calling
	-doHetPlas	Estimate hetplasmy by calculating a pooled haploid frequency

	Below are options that can be usefull
	-bam		Options relating to bam reading
	-doMajorMinor	Infer the major/minor using different approaches
	-ref/-anc	Read reference or ancestral genome
	-doSNPstat	Calculate various SNPstat
	-cigstat	Printout CIGAR stat across readlength
	many others

Output files:
	 In general the specific analysis outputs specific files, but we support basic bcf output
	-doBcf		Wrapper around -dopost -domajorminor -dofreq -gl -dovcf docounts
For information of specific options type: 
	./angsd METHODNAME eg 
		./angsd -GL
		./angsd -doMaf
		./angsd -doAsso etc
		./angsd sites for information about indexing -sites files
Examples:
	Estimate MAF for bam files in 'list'
		'./angsd -bam list -GL 2 -doMaf 2 -out RES -doMajorMinor 1'

Using Multiple Cores/Threads

The angsd application allows you define multiple cores/threads within calls using the '-nThreads or -P for number of threads allocated to the program' options.

Following the examples, a batch script would take the following form where we are defining and using 8 cores (on a single node).

#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=8
...
module load gcc/7.3.0
module load angsd/0.935
...
angsd -b bam.filelist -GL 1 -doMajorMinor 1 -doMaf 2 -P 8

The best number of cores/threads to use for a particular job will depend on the type of sequencing/data and is up to the researcher to explore.

Please feel free to report/share any interesting observations and we can update this page.

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