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  • bwa sampe - playing with the parameters?

    Hi, I'm just looking for input from the SEQ community, has anyone tinkered with any of the parameters for
    bwa sampe
    e.g. -a, -n, -N
    and noticeably improved their results.

    I've got standard Illumina paired end, good QC, running it through the GATK pipeline, good results but I've only ever run the default bwa sampe options, just revising my pipeline and wondering if changing anything here will improve my results, e.g. I don't have a feel for how increasing the number of hits to output for paired reads will impact on my final VCF file.

    Thanks.

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