X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=NEWS;h=6c2195e5929fab1dbe96b5fafc734a62443ec99c;hp=28d6aaa81269b72f0b8cb26a971c5bd55e33c050;hb=016b50ab60e879a0b8f81cb76ce11ea360a03d4a;hpb=cb12a866906ec4ac644de0e658679261c82ab098

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+Beta Release 0.1.10 (16 November, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This release is featured as the first major improvement to the indel
+caller. The method is similar to the old one implemented in the pileup
+command, but the details are handled more carefully both in theory and
+in practice. As a result, the new indel caller usually gives more
+accurate indel calls, though at the cost of sensitivity. The caller is
+implemented in the mpileup command and is invoked by default. It works
+with multiple samples.
+
+Other notable changes:
+
+ * With the -r option, the calmd command writes the difference between
+   the original base quality and the BAQ capped base quality at the BQ
+   tag but does not modify the base quality. Please use -Ar to overwrite
+   the original base quality (the 0.1.9 behavior).
+
+ * Allow to set a maximum per-sample read depth to reduce memory. In
+   0.1.9, most of memory is wasted for the ultra high read depth in some
+   regions (e.g. the chr1 centromere).
+
+ * Optionally write per-sample read depth and per-sample strand bias
+   P-value.
+
+ * Compute equal-tail (Bayesian) credible interval of site allele
+   frequency at the CI95 VCF annotation.
+
+ * Merged the vcfutils.pl varFilter and filter4vcf for better SNP/indel
+   filtering.
+
+(0.1.10: 16 November 2010, r829)
+
+
+
+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 0.1.8 (11 July, 2010)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~