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  • hrseq
    Junior Member
    • Aug 2011
    • 5
    #1

    bwa-mem artifact with deletions

    Hi

    when I run bwa-mem with the options "-w 100 -O 5 -E 0.4" on paired end data I get the distribution of deletion sizes as shown in the attached image.

    Can anybody give a hint where this spiky pattern comes from? It is not observed when aligning with bwa-aln or bowtie2, so it does not seem to be due to the sample. Any hint would be welcome.

    best regards
    hubert
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