Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

How can I make/or get interval file?

pmintpmint Member

Do I have to make the interval file for --intervals option in muTect?
or is it made during picard/GATK process?

Best Answer

Answers

  • pmintpmint Member

    Then, '... combine your reference file's sequence dictionary ( .dict ) and interval
    file ..'
    interval file <-- that is made during RealignTargetCreator, right?

  • bd5fh2bd5fh2 Member

    Hi,
    I have two issues with running MuTect:

    1. I read this post "What input files does the GATK accept?" at http://gatkforums.broadinstitute.org/discussion/1204/what-input-files-does-the-gatk-accept, specifically at #3, Intervals. Copying the example given in the post, I still get the same error from MuTect as with my own interval file:
    ERROR MESSAGE: File associated with name /data/wangj14/refData/gatk/hg19/mock.interval_list is malformed: Interval file could not be parsed in any supported format. caused by Failed to parse Genome Location string: @HD VN:1.0 SO:coordinate

    I also tried other variations on this header line "@HD VN:1.0 SO:coordinate" and always got the same error message. It appears that MuTect jar doesn't like "@HD\tVN:1.0".

    1. On a separate note, I read somewhere on a MuTect documentation that the interval can be like this:
      chr1:30366-30503
      chr1:69089-70010

    But the example given is like this:
    1 30366 30503 + target_1
    1 69089 70010 + target_2
    1 367657 368599 + target_3
    1 621094 622036 + target_4
    1 861320 861395 + target_5
    1 865533 865718 + target_6
    ...

    Which one of these is correct or both?

    Thank you.

Sign In or Register to comment.