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Download the latest Picard release at https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

MuTect source now available in GitHub!

kcibulkcibul Cambridge, MAMember, Broadie, Dev
edited December 2015 in MuTect v1 Documentation

Please note that this article refers to the original standalone version of MuTect. A new version is now available within GATK (starting at GATK 3.5) under the name MuTect2. This new version is able to call both SNPs and indels. See the GATK version 3.5 release notes and the MuTect2 tool documentation for further details.

The MuTect source code is now available as a GitHub repository (https://github.com/broadinstitute/mutect). If you wish to build from source, please read the build instructions carefully as we are currently building against a tag (v2.5) of the gatk-protected repository. We'll be moving to 2.6 soon (which is based on Java 7). We'll be doing some cleanup as we move from our internal source control and environment to a more open environment, but wanted to make the code available sooner rather than later.

Of course, please make sure that you abide by the terms of the license agreement which is in each file header as well as in the GitHub repository https://github.com/broadinstitute/mutect/blob/master/mutect.LICENSE.TXT

Thanks, and please let us know if you find any problems

Post edited by Geraldine_VdAuwera on
Tagged:

Answers

  • igorigor New YorkMember

    Is the source posted on GitHub considered stable or is that more of a development version? Should it be used instead of version 1.1.4 that's posted on the MuTect website or is it just for testing?

  • Greetings,

    Two items:

    1) I've been trying to build but run into this problem:

    [cll@cfdna mutect-src]$ git clone git@github.com:broadinstitute:mutect.git
    Initialized empty Git repository in /home/shared/ngs_tools/mutect-src/mutect/.git/
    ERROR: Repository invalid.
    fatal: The remote end hung up unexpectedly
    

    Has the repository moved?

    2) A comment to the issue with the java version above - there may be multiple versions of java installed on the machine. If this is in a linux environment, running update-alternatives as follows (my environment is Red Hat) may help:

    [cll@cfdna mutect-src]$ update-alternatives --config javac
    
    There are 2 programs which provide 'javac'.
    
      Selection    Command
    -----------------------------------------------
       1           /usr/lib/jvm/java-1.6.0-openjdk.x86_64/bin/javac
    *+ 2           /usr/lib/jvm/java-1.7.0-openjdk.x86_64/bin/javac
    

    Thanks,
    CLL

  • schauserschauser denmarkMember

    Dear Mutect team,

    Do people outside the Broad network have access to indelocator download? The git repository produces errors both using git clone git@github.com:broadinstitute/indelocator and using git clone https://github.com/broadinstitute/indelocator.

    Thanks Leif

  • JiantaoShiJiantaoShi BostonMember

    You can use gatk-2.3-9-gdcdccbb which contains SomaticIndelDetector. It should be the same as indelocator.

    Jiantao

    @schauser said:
    Dear Mutect team,

    Do people outside the Broad network have access to indelocator download? The git repository produces errors both using git clone git@github.com:broadinstitute/indelocator and using git clone https://github.com/broadinstitute/indelocator.

    Thanks Leif

  • rdeborjardeborja TorontoMember

    After building the git version of Mutect using Java 7 and following the instructions provided (including changing the ant command to use dist instead of package), I can't seem to find the Mutect jar file (find . | grep -i mutect | grep jar) in either the mutect-src or the gatk-protected directories. The build did work successfully according to the output from the ant command.

  • libolibo Member

    I share the same problem with rdeborja. I have compiled the source files from gatk-protected directory, using either dist or package in ant, but nothing appeared in the dist/packages/ directory. The compilation went successful and I don't know where it goes wrong. Thanks!

  • xhao79xhao79 Member

    i have install the mutect ,but after output some result than call a problem

    Error processing chr1:1317693
    java.lang.IllegalArgumentException: Comparison method violates its general contract!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi @xhao79‌, can you tell me what version you are using and what was your command line? Also, have you validated your bam files to make sure they have no problems?

  • sphsmithsphsmith United StatesMember

    Hello - I have tried using the pre-compiled binaries for mutect 1.1.1 and 1.1.4, using the current GATK references and those provided on the MuTect download page. I am running on the same system we use GATK tools commonly. The run appears to proceed fine with the usual ProgressMeter log output, then NSRuntimeProfile log output, but I get nothing in the output file or the wig file except their respective headers.

    I do have two WARN messages in my log file - one for the format of the leftAligned vcf provided on the muTect site:
    WARN 13:44:15,372 VCFStandardHeaderLines$Standards - Repairing standard header line for field AF because -- count types disagree; header has UNBOUNDED but standard is A -- descriptions disagree; header has 'Allele Frequency' but standard is 'Allele Frequency, for each ALT allele, in the same order as listed'

    and one for ET:
    WARN 13:46:51,224 RestStorageService - Error Response: PUT '/GATK_Run_Reports/goNhQwyP7zbzvm4jDsJuUP3eULLSzqSH.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 415, Content-MD5: B0o2qLxRd5sWVrqpFZ0iBQ==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: 074a36a8bc51779b1656baa9159d2205, Date: Mon, 28 Jul 2014 18:46:50 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:ApDI9KtjG7HBKJPVVesSgZULCSY=, User-Agent: JetS3t/0.8.1 (Linux/2.6.18-194.32.1.el5_TACC; amd64; en; JVM 1.7.0_45), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: EDC78AB511BFD8B6, x-amz-id-2: lX2THuE10Yphvq2SJcA2h6EWxKGcRaVefE6JQl0sl+peQ2C2wQC3F/PmvX9Lc+2u, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Mon, 28 Jul 2014 18:46:50 GMT, Connection: close, Server: AmazonS3]

    Same error regardless of 1.1.1 or 1.1.4, and again on a system I've just run GATK 2.8 on with no problem (in fact, tested a second system - same error, and has been occurring since last Friday).

    These are real biological samples, so I am not sure whether no data means no mutations, or that the program hasn't run correctly.

    Any suggestions? Is there sample data to test installation?

    Thank you!
    -Scott

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Scott @sphsmith‌

    The first warning is trivial, shouldn't cause any problems. For the second, it's a problem with a deprecated component of the old GATK which the precompiled MuTects were built on. I think the latest MuTect source compiles against a recent enough version of GATK to bypass the problem; if not you'll have to request a key to deactivate the phone home system. See http://www.broadinstitute.org/gatk/blog?id=4251 for more details.

  • sphsmithsphsmith United StatesMember

    Thanks Geraldine - I requested and received the key but after using -et NO_ET and -K , I get:

    ERROR ------------------------------------------------------------------------------------------
    ERROR stack trace

    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Could not locate the GATK public key GATK_public.key in the classpath
    at org.broadinstitute.sting.utils.crypt.CryptUtils.loadGATKDistributedPublicKey(CryptUtils.java:278)
    at org.broadinstitute.sting.gatk.CommandLineExecutable.authorizeGATKRun(CommandLineExecutable.java:137)
    at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:85)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
    at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 2.1-202-g2fe6a31):
    ERROR
    ERROR Please visit the wiki to see if this is a known problem
    ERROR If not, please post the error, with stack trace, to the GATK forum
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ERROR
    ERROR MESSAGE: Could not locate the GATK public key GATK_public.key in the classpath
    ERROR ------------------------------------------------------------------------------------------

    (same error from both versions, two different computers, independent downloads)

    Searching around the support pages, it looks like this means that muTect 1.1.1 & 1.1.4 won't support the -K option because they weren't compiled against the right GATK?

    Is the only option to create a working muTect to start from source?

    Thank you,
    Scott

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Ah, I hadn't thought of that, sorry. That's right, you'll have to compile from the latest source. I'll see if we can make a precompiled binary available since this is going to be a problem for lots of people going forward. In the meantime, you can find build instructions here: https://github.com/broadinstitute/mutect

    Let me know if you have any issues.

  • xhao79xhao79 Member

    java -jar muTect-1.1.4.jar --analysis_type MuTect --reference_sequence ../hg19_37/hg19_v37.fa --cosmic cosmic.vcf --dbsnp dbsnp.vcf --input_file:normal ../Sample_2014-S02011/2011.sorted.bam --input_file:tumor ../Sample_2014-S02012/2012.sorted.bam --out 12vs11.out --coverage_file 12vs11.cov.txt
    use this command ,error message is
    rror processing chr1:1317616
    java.lang.IllegalArgumentException: Comparison method violates its general contract!

    but i use GATK command above have no mistake ,so i think bam file have no problem
    java -jar /home/software/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar -T UnifiedGenotyper -R ../hg19_37/hg19_v37.fa -I ../Sample_2014-S02012/2012.sorted.bam -nt 40 -o test.vcf

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    @xhao79‌ I've posted a compiled binary of the latest version of MuTect (1.1.7) here:

    http://www.broadinstitute.org/gatk/temp/mutect-1.1.7.jar

    Can you please download it and try it to see if the error still happens with the newer version?

  • lletournlletourn montrealMember

    I had the same problems that @libo and @rdeborja had on mutect 1.1.6 until I realised I needed to do git checkout 1.1.6 on mutects sources to build the tagged version. Just in case others hit this issue.

  • xhao79xhao79 Member

    @Geraldine_VdAuwera thank you very much , but the argument --input_file:normal --input_file:tumor can not be used in the new version?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    @xhao79‌ That should still work -- are you getting an error message when you use this? Can you tell me what is the error message?

  • MattBMattB NewcastleMember

    Hi Geraldine, re the link above for the compiled MuTect 1.1.7 jar when looking over the output I actually find it reporting version 1.1.6: VERSION INFO: MuTect:1.1.6-3-g5c24107 Gatk:3.1-0-g72492bb

  • hbergerhberger MPI Infection biology, BerlinMember

    Just in case someone wants to run MuTect version 1.1.4 (the one currently available in CGA) with Java7, the error mentioned above can be avoided by forcing the older Java6 standard sorting algorithm. Just add "-Djava.util.Arrays.useLegacyMergeSort=true" right before -jar on the command line. (Credits for this fix: http://dertompson.com/2012/11/23/sort-algorithm-changes-in-java-7/)

  • jiujiezzjiujiezz ChinaMember

    @Geraldine_VdAuwera‌
    Hi Geraldine, the link is not available now, would you please post it again?
    Thanks a lot!

    @Geraldine_VdAuwera said:
    xhao79‌ I've posted a compiled binary of the latest version of MuTect (1.1.7) here:

    http://www.broadinstitute.org/gatk/temp/mutect-1.1.7.jar

    Can you please download it and try it to see if the error still happens with the newer version?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    We're rearranging how we provide non-GATK software, so hopefully we can start providing this again in the near future. In the meantime, you can get the latest MuTect from its github repository. The compilation instructions are in the readme document on github.

  • Wouldn't making the latest version available via a wget command be the easiest thing to do? ftp seems to be a good solution.

    I'm getting empty output files using 1.1.1 and 1.1.4
    log doesn't really give much help on troubleshooting this.

    So, I try and download "the latest mutect" following the instructions at github ...

    I get this error message ...
    -bash-4.1$ git clone git@github.com:broadinstitute/mutect.git
    Initialized empty Git repository in /data/data04/rich/MU/mutect-src/mutect/.git/
    Warning: Permanently added the RSA host key for IP address '192.30.252.129' to the list of known hosts.
    Permission denied (publickey).
    fatal: The remote end hung up unexpectedly

    Is this blocked?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Alright, I added MuTect 1.1.7 to the GATK downloads page as a temporary measure so you folks can get on with your work while we figure out how we want to set this up for the long term. Let me know if you have any issues.

  • 1.1.7 appears to be much better. Thank you.
    1.1.4 and 1.1.1 ran but did not produce any output beyond the headers.
    I recommend others with the "No Output" problem use 1.1.7 mutect.

  • Dear MuTect developers, I have the following questions:
    1. When is MuTect version 2 is going to be released?
    2. Is version 1.1.4 still the latest official one (according to this web page https://www.broadinstitute.org/cancer/cga/mutect_download)
    Thanks in advance!
    Katja

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    1. No guarantees, but we're looking at an October/November timeframe for MuTect 2.

    2. The latest public version is 1.1.7, available precompiled on the GATK downloads page.

  • bioxujintianbioxujintian GenomicsMember

    Dear MuTect developers, I have the following error:
    [xujt@fat-48 MuTect]$ git clone git@github.com:broadinstitute/mutect.git
    Initialized empty Git repository in /share/disk1/xujt/software/MuTect/mutect/.git/
    Warning: Permanently added the RSA host key for IP address '192.30.252.129' to the list of known hosts.
    Permission denied (publickey).
    fatal: The remote end hung up unexpectedly
    Thanks,
    xujintian

  • jingmengjingmeng AustraliaMember

    @bioxujintian said:
    Dear MuTect developers, I have the following error:
    [xujt@fat-48 MuTect]$ git clone git@github.com:broadinstitute/mutect.git
    Initialized empty Git repository in /share/disk1/xujt/software/MuTect/mutect/.git/
    Warning: Permanently added the RSA host key for IP address '192.30.252.129' to the list of known hosts.
    Permission denied (publickey).
    fatal: The remote end hung up unexpectedly
    Thanks,
    xujintian

    Please look at this link. http://gatkforums.broadinstitute.org/discussion/comment/25433#Comment_25433

  • @Geraldine_VdAuwera said:
    1. No guarantees, but we're looking at an October/November timeframe for MuTect 2.

    1. The latest public version is 1.1.7, available precompiled on the GATK downloads page.

    Dear Geraldine,

    Do you know if Mutect version 2 is close to release?

    Best regards
    Katja

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Katja, MuTect2 has been released as part of GATK 3.5, so it's available now.

  • @Geraldine_VdAuwera said:
    Hi Katja, MuTect2 has been released as part of GATK 3.5, so it's available now.

    Thank you very much Geraldine!
    I downloaded it now but I can't see any documentation. Do you know if there exists any?

    Best regards
    Katja

  • @Katja said:

    @Geraldine_VdAuwera said:
    Hi Katja, MuTect2 has been released as part of GATK 3.5, so it's available now.

    Thank you very much Geraldine!
    I downloaded it now but I can't see any documentation. Do you know if there exists any?

    Best regards
    Katja

    Sorry, my bad, found it here:
    http://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php

  • YingLiuYingLiu ChinaMember

    HI ,
    do people know how to filter Mutect results ?

  • vectoriovectorio BeijingMember

    Hi all,

    Everytime I hit the button to download MuTect1, on the download website, I end up with a blank page and nothing is happening, no download. Are there some maintenance going on ?

    David.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    @vectorio Sorry about that, there was a bug that crept in during a recent update. It's fixed now -- let us know if you experience any further difficulties.

  • vectoriovectorio BeijingMember
    Alright. Now it downloads correctly, thx.

    David.
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