https://github.com/broadinstitute/mutect

MuTect -- Accurate and sensitive cancer mutation detection
https://github.com/broadinstitute/mutect

Last synced: about 1 month 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 (10 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
• 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