Installation:

===== Program for analysing NGS data.

http://www.popgen.dk/angsd

Installation:

Using a local folder containing htslib

#download htslib
git clone --recurse-submodules https://github.com/samtools/htslib.git;
#download angsd
git clone https://github.com/angsd/angsd.git;

#install htslib
cd htslib
make

#install angsd
cd ../angsd
make HTSSRC=../htslib

Systemwide installation of htslib

git clone https://github.com/angsd/angsd.git;
cd angsd; make HTSSRC=systemwide

Using htslib submodule

git clone https://github.com/angsd/angsd.git;
cd angsd; make

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.
If you are on a mac computer and the compilation process complains about a missnig crybtolib library then do 'make CRYPTOLIB=""'

Program has a paper

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

Name		Name	Last commit message	Last commit date
Latest commit History 1,572 Commits
.github/workflows		.github/workflows
R		R
RES		RES
doc		doc
htslib @ e769401		htslib @ e769401
misc		misc
scripts		scripts
test		test
.gitignore		.gitignore
.gitmodules		.gitmodules
AUTHORS		AUTHORS
INSTALL		INSTALL
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
abcDstat2.cpp		abcDstat2.cpp
abcDstat2.h		abcDstat2.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
abcHWE_F.cpp		abcHWE_F.cpp
abcHWE_F.h		abcHWE_F.h
abcHaploCall.cpp		abcHaploCall.cpp
abcHaploCall.h		abcHaploCall.h
abcHetPlas.cpp		abcHetPlas.cpp
abcHetPlas.h		abcHetPlas.h
abcIBS.cpp		abcIBS.cpp
abcIBS.h		abcIBS.h
abcMajorMinor.cpp		abcMajorMinor.cpp
abcMajorMinor.h		abcMajorMinor.h
abcMcall.cpp		abcMcall.cpp
abcMcall.h		abcMcall.h
abcMismatch.cpp		abcMismatch.cpp
abcMismatch.h		abcMismatch.h
abcPSMC.cpp		abcPSMC.cpp
abcPSMC.h		abcPSMC.h
abcRAD.cpp		abcRAD.cpp
abcRAD.h		abcRAD.h
abcSaf.cpp		abcSaf.cpp
abcSaf.h		abcSaf.h
abcScounts.cpp		abcScounts.cpp
abcScounts.h		abcScounts.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
abcTemplate2.cpp		abcTemplate2.cpp
abcTemplate2.h		abcTemplate2.h
abcWriteBcf.cpp		abcWriteBcf.cpp
abcWriteBcf.h		abcWriteBcf.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
aio.cpp		aio.cpp
aio.h		aio.h
analysisFunction.cpp		analysisFunction.cpp
analysisFunction.h		analysisFunction.h
ancestral_likes.cpp		ancestral_likes.cpp
ancestral_likes.h		ancestral_likes.h
angsd.cpp		angsd.cpp
argStruct.cpp		argStruct.cpp
argStruct.h		argStruct.h
bam_likes.cpp		bam_likes.cpp
bam_likes.h		bam_likes.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

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