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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.

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