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  • BED to RefSeq gene format

    Hello,

    I would like to convert a BED interval file to RefSeq format. I need this to use it among with GATK DepthOfCoverage.

    I've been trying loading custom track on UCSC. (http://genome.ucsc.edu/cgi-bin/hgTables) to get it converted without success.

    Any tips?

  • #2
    "GATK accept interval files for processing subsets of the genome in Picard-style interval lists"


    I think you just need to change your bed file to <Picard-style interval> format.

    Comment


    • #3
      Indeed it accepts -L option for specify intervals. But I want per gene coverage report. That's why I need to generate RefSeq file from BED.

      Comment


      • #4
        Hi gmarco, did u find the answer to your qeustion?? If yes please share it.

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