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  • #1

    How to find structure variations from paired end sequencing in SAM format

    hello, everyone.
    I used software bwa to align my PE sequence to the reference, and got the alignments in SAM format.
    But I could not extract SV results from SAM formats.

    I find that BreakDancer (http://genome.wustl.edu/tools/cancer...etection-tools) or maq.pl can directly find SV from alignments in maq mapview format.
    I wonder if there is any tool like this for SAM format, or if there is any tools that can translate SAM format into MAQ mapview format.

    Thank you all.
    Tags: bwa, paired end, sam, structure variation
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