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  • Release notes of SAMtool-0.1.9

    A shameless promotion...

    Beta Release 0.1.9 (27 October, 2010)
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

    This release is featured as the first major improvement to the samtools'
    SNP caller. It comes with a revised MAQ error model, the support of
    multi-sample SNP calling and the computation of base alignment quality
    (BAQ).

    The revised MAQ error model is based on the original model. It solves an
    issue of miscalling SNPs in repetitive regions. Althought such SNPs can
    usually be filtered at a later step, they mess up unfiltered calls. This
    is a theoretical flaw in the original model. The revised MAQ model
    deprecates the orginal MAQ model and the simplified SOAPsnp model.

    Multi-sample SNP calling is separated in two steps. The first is done by
    samtools mpileup and the second by a new program, bcftools, which is
    included in the samtools source code tree. Multi-sample SNP calling also
    works for single sample and has the advantage of enabling more powerful
    filtration. It is likely to deprecate pileup in future once a proper
    indel calling method is implemented.

    BAQ is the Phred-scaled probability of a read base being wrongly
    aligned. Capping base quality by BAQ has been shown to be very effective
    in suppressing false SNPs caused by misalignments around indels or in
    low-complexity regions with acceptable compromise on computation
    time. This strategy is highly recommended and can be used with other SNP
    callers as well.

    In addition to the three major improvements, other notable changes are:

    * Changes to the pileup format. A reference skip (the N CIGAR operator)
    is shown as '<' or '>' depending on the strand. Tview is also changed
    accordingly.

    * Accelerated pileup. The plain pileup is about 50% faster.

    * Regional merge. The merge command now accepts a new option to merge
    files in a specified region.

    * Fixed a bug in bgzip and razip which causes source files to be
    deleted even if option -c is applied.

    * In APIs, propogate errors to downstream callers and make samtools
    return non-zero values once errors occur.

    (0.1.9: 27 October 2010, r783)

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