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  • samtools -view region (overlap?) question

    hello,

    does somebody know how overlap is definded for the
    samtools view region
    function.

    given the defined region # and four reads a-d:
    Code:
                        ##############################
                    aaaaaaaaaaaaaaaaa
                        bbbbbbbbbbbbbbbb
                                   ccccccccccccccccccc
                                            ddddddddddddddd
    which one is extracted: b and c or a-d?


    thank you,

    dietmar

  • #2
    No idea, but it should not be difficult to test by browsing a real bal file with the "samtools tview" option and selecting the first region with a couple of overlapping reads. I bet on a-d

    Comment


    • #3
      I think it should give you all of them - any reads within or overlapping the region requested.

      Comment


      • #4
        further question

        I think it should give you all of them - any reads within or overlapping the region requested.
        this seems true, all overlapping were extracted.

        does somebody know a script to fetch only those which start AND end inside a given range (###).

        Code:
                            #################################
                        aaaaaaaaaaaaaaaaa
                            bbbbbbbbbbbbbbbb
                                       ccccccccccccccccccc
                                                ddddddddddddddd
        eeee----splice------eeeeeeeeeee
        here only: b and c

        Comment


        • #5
          You might consider using BEDTools instead of samtools view. BEDTools can be given a .bed file of intervals, and a .bam file, and you could limit the reads to only those which completely overlap the intervals.

          Comment


          • #6
            @swbarnes

            thank you, works great, but too slow with big bam files:

            therefore preselection with samtools...

            Code:
            samtools view -b xxx.bam chr1:1000-2000 | bedtools intersect -f 1.0 -b region.bed -abam - | samtools view - > yyy.sam

            Comment

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