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  • query read by read name

    Hello,
    I am using picard library in java.
    is it possible to make query for a specific readname in a bam file?

    thanks
    Yu

  • #2
    Originally posted by jay2008 View Post
    Hello,
    I am using picard library in java.
    is it possible to make query for a specific readname in a bam file?

    thanks
    Yu
    If you just want one or few reads you could do:

    Code:
    samtools view myaln.bam | grep '^myreadname'
    Dario

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    • #3
      I meant what the API in picard can be used.

      Comment


      • #4
        Originally posted by jay2008 View Post
        I meant what the API in picard can be used.
        Not sure if it is possible in picard. If helpful, consider that you can send the output of picard to stdout using /dev/stdout as output file and then you could pipe it to samtools or grep. If you can be more specific about what you want to achieve you could get more helpful answers...

        Dario

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        • #5
          bam file can be sorted in two ways: coordinate and queryname (sorted by read name). bam.query is based on coordinate. I can not find any APIs for bam file sorted by queryname. I guess there should be search APIs...

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