X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=NEWS;h=6c2195e5929fab1dbe96b5fafc734a62443ec99c;hp=8db09960a431676632e7e03649f17001076ddf06;hb=016b50ab60e879a0b8f81cb76ce11ea360a03d4a;hpb=317f5e8dd22cc9e1e5e05fbcaeb3b9aca7447351 diff --git a/NEWS b/NEWS index 8db0996..6c2195e 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,166 @@ +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) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Notable functional changes: + + * Added the `reheader' command which replaces a BAM header with a new + header. This command is much faster than replacing header by + BAM->SAM->BAM conversions. + + * Added the `mpileup' command which computes the pileup of multiple + alignments. + + * The `index' command now stores the number of mapped and unmapped + reads in the index file. This information can be retrieved quickly by + the new `idxstats' command. + + * By default, pileup used the SOAPsnp model for SNP calling. This + avoids the floating overflow in the MAQ model which leads to spurious + calls in repetitive regions, although these calls will be immediately + filtered by varFilter. + + * The `tview' command now correctly handles CIGARs like 7I10M and + 10M1P1I10M which cause assertion failure in earlier versions. + + * Tview accepts a region like `=10,000' where `=' stands for the + current sequence name. This saves typing for long sequence names. + + * Added the `-d' option to `pileup' which avoids slow indel calling + in ultradeep regions by subsampling reads locally. + + * Added the `-R' option to `view' which retrieves alignments in read + groups listed in the specified file. + +Performance improvements: + + * The BAM->SAM conversion is up to twice faster, depending on the + characteristic of the input. + + * Parsing SAM headers with a lot of reference sequences is now much + faster. + + * The number of lseek() calls per query is reduced when the query + region contains no read alignments. + +Bug fixes: + + * Fixed an issue in the indel caller that leads to miscall of indels. + Note that this solution may not work well when the sequencing indel + error rate is higher than the rate of SNPs. + + * Fixed another issue in the indel caller which may lead to incorrect + genotype. + + * Fixed a bug in `sort' when option `-o' is applied. + + * Fixed a bug in `view -r'. + +APIs and other changes: + + * Added iterator interfaces to random access and pileup. The callback + interfaces directly call the iterator interfaces. + + * The BGZF blocks holding the BAM header are indepedent of alignment + BGZF blocks. Alignment records shorter than 64kB is guaranteed to be + fully contained in one BGZF block. This change is fully compatible + with the old version of samtools/picard. + +Changes in other utilities: + + * Updated export2sam.pl by Chris Saunders. + + * Improved the sam2vcf.pl script. + + * Added a Python version of varfilter.py by Aylwyn Scally. + +(0.1.8: 11 July 2010, r613) + + + Beta Release 0.1.7 (10 November, 2009) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~