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  • Convert merged BAM back to per lane BAM or FASTQ file

    I have got some illumina data in a a merged BAM file for a particular sample and I would like to convert it back to per lane data files (BAM or fastq) so it would be compatible with the analysis pipeline. Any ideas on the best way to do this?

  • #2
    When I did this a few days ago (with only knowledge of command-line stuff and samtools), here's a rough guide to what I did:
    1. Extract header from BAM file
      Code:
      samtools view -H infile.bam > header.sam
    2. filter out lanes from BAM file, add header
      Code:
      (cat header.sam; samtools view infile.bam | grep '^DATA...._<lane>_.') > out_lane<lane>.sam
    3. convert SAM to BAM
      Code:
      samtools view -S out_lane<lane>.sam -b > out_lane<lane>.bam


    There's probably some better way, but it would have taken longer for me to find than for me to just do it and deal with the additional overhead of storing temporary SAM files per lane.

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    • #3
      If the lane info is stored in RG tags you can use this: http://genome.sph.umich.edu/wiki/SplitBam

      Comment


      • #4
        SplitBam looks ideal, but I can't find a download link for it. Any ideas?

        And thanks for the other suggestion too, that makes a lot of sense.

        --EDIT--
        Actually it looks like there are no @RG in the headers ... Oh Dear.
        Last edited by danielsbrewer; 09-29-2011, 01:03 AM.

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        • #5
          SplitBam download link?

          I am trying to do the exact same thing and I do have @RG tags, but I can not find a download link for SplitBam. Does anyone know how to download this program?

          Jason

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          • #6
            Originally posted by danielsbrewer View Post
            SplitBam looks ideal, but I can't find a download link for it. Any ideas?

            And thanks for the other suggestion too, that makes a lot of sense.

            --EDIT--
            Actually it looks like there are no @RG in the headers ... Oh Dear.
            Originally posted by jtladner View Post
            I am trying to do the exact same thing and I do have @RG tags, but I can not find a download link for SplitBam. Does anyone know how to download this program?

            Jason
            Go here and either follow the instructions for retrieving the current development release from the source repository or download the tarball for the latest stable realese (0.1.4). Note that either way you are downloading the entire libStatGen toolkit, which you must then compile. SplitBam is merely one of the programs in the toolkit.

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            • #7
              Originally posted by jtladner View Post
              I am trying to do the exact same thing and I do have @RG tags, but I can not find a download link for SplitBam. Does anyone know how to download this program?

              Jason


              splitBam is part of the bamUtil package, which i found it here https://github.com/Homebrew/homebrew-science and it was very easy to download it.

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