GitHub - wtsi-npg/Gftools: A set of utilities to handle individual-level genotype data files

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A set of utilities to handle individual-level genotype data files

gftools.sourceforge.net

GPL-3.0 license

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Name		Name	Last commit message	Last commit date
Latest commit History 43 Commits
.gitignore		.gitignore
LICENSE.txt		LICENSE.txt
Makefile		Makefile
README.txt		README.txt
VERSION		VERSION
bed_to_tped.cpp		bed_to_tped.cpp
data.bed		data.bed
data.bim		data.bim
data.fam		data.fam
empty.bed		empty.bed
empty.bim		empty.bim
empty.fam		empty.fam
exceptions.h		exceptions.h
individual.h		individual.h
pairwise_concordance_bed.cpp		pairwise_concordance_bed.cpp
plink_binary.cpp		plink_binary.cpp
plink_binary.h		plink_binary.h
plink_binary.i		plink_binary.i
plink_binary_to_tab.cpp		plink_binary_to_tab.cpp
snp.h		snp.h
snp_af_sample_cr_bed.cpp		snp_af_sample_cr_bed.cpp
tab_to_plink_binary.cpp		tab_to_plink_binary.cpp
test_plink_binary.h		test_plink_binary.h
tped_to_bed		tped_to_bed
utilities.cpp		utilities.cpp
utilities.h		utilities.h

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This is a development fork of the gftools library. The repository at
http://gftools.sourceforge.net/ is no longer maintained by the author.

Installation:
make install PREFIX=<install-directory>


Gftools requires the Plink software package.
See http://pngu.mgh.harvard.edu/~purcell/plink/

Gftools is required for The Wellcome Trust Sanger Institute (WTSI) 
genotyping pipeline, including the standalone gender check.
See https://github.com/wtsi-npg/genotyping

The version of the Illuminus genotype caller used at WTSI depends on gftools.
See https://github.com/keithj/Illuminus