software tool for the manipulation, annotation, selection, simulation, and analysis of variants in the context of next-gen sequencing analysis
C Python C++ Other
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annotation Document test utilites Jan 14, 2016
cgatools Normalize indels using reference genome information during variant im… Jan 7, 2016
development Add a Dockerfile for variant tools, which relies on simuPOP (for vtoo… May 9, 2016
format fix a duplicate line in vcf.fmt Jan 24, 2014
gsl Build supporting libraries as separate libraries to avoid repeated co… Feb 10, 2016
libplinkio update libplinkio to allow for fam file 'sex' column to use any chara… Nov 19, 2013
pipeline Minor update to pipeline Oct 29, 2015
rext add --skip column to SKAT meta analysis script PFF version; fix a cou… May 13, 2013
simulation Fix an error caused by cyclic import May 9, 2016
sqlite Suppress all third-party warning messages Feb 10, 2016
test Improve tests in test_init.py Jan 25, 2016
ucsc Build supporting libraries as separate libraries to avoid repeated co… Feb 10, 2016
utility Fix parameter max_jobs of submit_jobs Sep 16, 2015
variant_tools Allow the specification of zero-based index for command vtools_report… Feb 21, 2017
.gitignore Stop tracking swig generated files because of different generated fil… Sep 27, 2015
MANIFEST.in Slightly reduce the size of source package by pruning some boost head… Jan 13, 2016
README Add an INSTALL file, and two single-file executables to macosx installer Apr 26, 2013
code_style.cfg Add uncrustify c++ code style configuration file Apr 12, 2012
setup.py Do not build local static libraries if they already exist. Feb 14, 2016
vtools Adding an extra level of debug logging called TRACE and move all prog… Jul 24, 2014
vtools_report Allow the specification of zero-based index for command vtools_report… Feb 21, 2017

README

This package contains variant tools, a command line tool for 
the manipulation, annotation, and analysis of genetic variants
from next-generation sequencing studies. Please refer to 
http://varianttools.sourceforge.net for details.