From: Heng Li <lh...@sa...> - 2010-10-28 02:58:34
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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) -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. |