angsd:

Program for analysing NGS data.

Installation:

git clone https://github.com/samtools/htslib.git; git clone https://github.com/angsd/angsd.git; cd angsd;make HTSDIR=../htslib

Notes

I've switched over to using htslib for parsing single reads (to allow for CRAM reading, while avoid having to write my own CRAM parser). I'm still using my own readpools. Users should therefore also download and install htslib.
http://www.popgen.dk/angsd/

Program has a paper

http://www.biomedcentral.com/1471-2105/15/356/abstract

Name		Name	Last commit message	Last commit date
Latest commit History 353 Commits
R		R
RES		RES
doc		doc
misc		misc
test		test
.travis.yml		.travis.yml
AUTHORS		AUTHORS
Makefile		Makefile
README.md		README.md
abc.cpp		abc.cpp
abc.h		abc.h
abcAncError.cpp		abcAncError.cpp
abcAncError.h		abcAncError.h
abcAncestry.cpp		abcAncestry.cpp
abcAncestry.h		abcAncestry.h
abcAsso.cpp		abcAsso.cpp
abcAsso.h		abcAsso.h
abcCallGenotypes.cpp		abcCallGenotypes.cpp
abcCallGenotypes.h		abcCallGenotypes.h
abcCounts.cpp		abcCounts.cpp
abcCounts.h		abcCounts.h
abcCovar.cpp		abcCovar.cpp
abcCovar.h		abcCovar.h
abcDstat.cpp		abcDstat.cpp
abcDstat.h		abcDstat.h
abcError.cpp		abcError.cpp
abcError.h		abcError.h
abcFilter.cpp		abcFilter.cpp
abcFilter.h		abcFilter.h
abcFilterSNP.cpp		abcFilterSNP.cpp
abcFilterSNP.h		abcFilterSNP.h
abcFreq.cpp		abcFreq.cpp
abcFreq.h		abcFreq.h
abcGL.cpp		abcGL.cpp
abcGL.h		abcGL.h
abcGetFasta.cpp		abcGetFasta.cpp
abcGetFasta.h		abcGetFasta.h
abcHWE.cpp		abcHWE.cpp
abcHWE.h		abcHWE.h
abcHetPlas.cpp		abcHetPlas.cpp
abcHetPlas.h		abcHetPlas.h
abcMajorMinor.cpp		abcMajorMinor.cpp
abcMajorMinor.h		abcMajorMinor.h
abcMismatch.cpp		abcMismatch.cpp
abcMismatch.h		abcMismatch.h
abcSaf.cpp		abcSaf.cpp
abcSaf.h		abcSaf.h
abcSaf2.cpp		abcSaf2.cpp
abcSaf2.h		abcSaf2.h
abcSmartCounts.cpp		abcSmartCounts.cpp
abcSmartCounts.h		abcSmartCounts.h
abcSnpTools.cpp		abcSnpTools.cpp
abcSnpTools.h		abcSnpTools.h
abcTemplate.cpp		abcTemplate.cpp
abcTemplate.h		abcTemplate.h
abcWriteFasta.cpp		abcWriteFasta.cpp
abcWriteFasta.h		abcWriteFasta.h
abcWritePlink.cpp		abcWritePlink.cpp
abcWritePlink.h		abcWritePlink.h
abcWriteVcf.cpp		abcWriteVcf.cpp
abcWriteVcf.h		abcWriteVcf.h
analysisFunction.cpp		analysisFunction.cpp
analysisFunction.h		analysisFunction.h
angsd.cpp		angsd.cpp
argStruct.h		argStruct.h
bam_likes.cpp		bam_likes.cpp
bam_likes.h		bam_likes.h
bam_md.c		bam_md.c
bam_md.h		bam_md.h
bambi_interface.h		bambi_interface.h
bammer_main.cpp		bammer_main.cpp
bammer_main.h		bammer_main.h
beagleReader.cpp		beagleReader.cpp
beagleReader.h		beagleReader.h
bfgs.cpp		bfgs.cpp
bfgs.h		bfgs.h
chisquare.cpp		chisquare.cpp
chisquare.h		chisquare.h
fet.c		fet.c
filterStrandBias.cpp		filterStrandBias.cpp
gatk_likes.cpp		gatk_likes.cpp
gatk_likes.h		gatk_likes.h
glfReader.cpp		glfReader.cpp
glfReader.h		glfReader.h
kprobaln.c		kprobaln.c
kprobaln.h		kprobaln.h
mUpPile.cpp		mUpPile.cpp
mUpPile.h		mUpPile.h
makeReadPool.cpp		makeReadPool.cpp
makeReadPool.h		makeReadPool.h
mpileup.cpp		mpileup.cpp
mpileup.h		mpileup.h
multiReader.cpp		multiReader.cpp
multiReader.h		multiReader.h
parseArgs_bambi.cpp		parseArgs_bambi.cpp
parseArgs_bambi.h		parseArgs_bambi.h
phys_likes.cpp		phys_likes.cpp
phys_likes.h		phys_likes.h
pooled_alloc.c		pooled_alloc.c
pooled_alloc.h		pooled_alloc.h

pdworzynski/angsd

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