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https://github.com/broadinstitute/mutect
MuTect -- Accurate and sensitive cancer mutation detection
https://github.com/broadinstitute/mutect
Last synced: 3 months ago
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MuTect -- Accurate and sensitive cancer mutation detection
- Host: GitHub
- URL: https://github.com/broadinstitute/mutect
- Owner: broadinstitute
- Created: 2013-01-29T15:09:43.000Z (almost 12 years ago)
- Default Branch: master
- Last Pushed: 2023-02-13T21:40:10.000Z (almost 2 years ago)
- Last Synced: 2024-02-15T09:33:35.593Z (12 months ago)
- Language: Java
- Homepage: http://www.broadinstitute.org/cancer/cga/mutect
- Size: 72.2 MB
- Stars: 92
- Watchers: 43
- Forks: 45
- Open Issues: 11
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Metadata Files:
- Readme: README.md
Awesome Lists containing this project
- AwesomeGenomics - Mutect1
- Awesome-Bioinformatics-Benchmarks - MuTect
README
Overview
--------------------------------------------------------
For complete details see
http://www.broadinstitute.org/cancer/cga/mutect
And for support please visit
http://gatkforums.broadinstitute.org/categories/mutect
How to build MuTect
--------------------------------------------------------
PREREQUISITES
To compile MuTect you must be using Java 1.7 and Maven 3.0+. After building successfully, the MuTect JAR file will be in mutect/target/mutect-*.jar
BUILD STEPS
# make a new source directory (e.g. mutect-src)
mkdir mutect-src
cd mutect-src
# get MuTect source
git clone [email protected]:broadinstitute/mutect.git
# get the GATK source and set to the latest tested version
git clone [email protected]:broadgsa/gatk-protected.git
cd gatk-protected
git reset --hard 3.1
# build the GATK first and install it to the local mvn repo. Once GATK publishes to a public repo this will be much simpler
mvn -Ddisable.queue install
# build MuTect and run unit tests (the target jar will be in target/mutect-*.jar)
cd ../mutect
mvn verify
# run integration tests, if you like
./run_regression.pl
./tieout_regression.pl