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  • MurielGB
    Member
    • Oct 2013
    • 51

    #1

    Obtain Read Group from Bam file

    Hello,
    Is it possible to obtain the read group of a bam file ?
    I am doing this by converting bam into sam (see below) but I would like to do it directly on the bam file because converting is long !
    Thanks a lot !

    #samtools view -h ${OUTPUT}.bam > ${OUTPUT}.bam.sam
    #grep "^@RG" ${OUTPUT}.bam.sam > RG_${OUTPUT}
  • dpryan
    Devon Ryan
    • Jul 2011
    • 3478

    #2
    Code:
    samtools view -H ${OUTPUT}.bam | grep "^@RG" >RG_${OUTPUT}
    You only need the header, so no need to output the whole thing.

    Comment

    • MurielGB
      Member
      • Oct 2013
      • 51

      #3
      Oh great !!
      Thanks a lot !

      Comment

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