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  • pirates.genome
    Member
    • Mar 2012
    • 11
    #1

    Filter paired & mapped reads from SAM/BAM file

    Hi,
    I have SAM/BAM files of paired end Illumina sequencing obtained by BWA.

    I want to filter out all reads having "proper pair" and both the reads of pair aligned to references. How can I filter them?

    Thanks in advance...
    Tags: None
  • dariober
    Senior Member
    • May 2010
    • 311
    #2
    Hi- This should filter out all the reads where both mates are mapped and the mates face each other (---> <---). (Make sure it does what you want!).

    Code:
    samtools view -F 2 input.bam > output.sam
    Best

    Dario

    Comment

    • pirates.genome
      Member
      • Mar 2012
      • 11
      #3
      Thats what I was looking for!

      Thank you Dario for the reply. I was looking for the same.

      Comment

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