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  • syfo
    Just a member
    • Nov 2012
    • 103

    #1

    BEDtools intersect output is BED instead of BAM

    Hi all,
    I want to discard the reads that overlap some blacklist regions, so I use
    intersectbed -abam -v -a readfile.bam -b badregions.bed

    I get 9 entries in BED format, despite the abam option ("The A input file is in BAM format. Output will be BAM as well.")

    Now if I add the -wa option I get 3.5M entries, again in BED format.

    Any idea about what is going on?
    thanks
  • syfo
    Just a member
    • Nov 2012
    • 103

    #2
    OK, the command line was wrong; it should have been
    intersectbed -v -abam readfile.bam -b badregions.bed
    problem solved

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