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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)
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)