1 Beta Release 0.1.10 (16 November, 2010)
2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
4 This release is featured as the first major improvement to the indel
5 caller. The method is similar to the old one implemented in the pileup
6 command, but the details are handled more carefully both in theory and
7 in practice. As a result, the new indel caller usually gives more
8 accurate indel calls, though at the cost of sensitivity. The caller is
9 implemented in the mpileup command and is invoked by default. It works
10 with multiple samples.
12 Other notable changes:
14 * With the -r option, the calmd command writes the difference between
15 the original base quality and the BAQ capped base quality at the BQ
16 tag but does not modify the base quality. Please use -Ar to overwrite
17 the original base quality (the 0.1.9 behavior).
19 * Allow to set a maximum per-sample read depth to reduce memory. In
20 0.1.9, most of memory is wasted for the ultra high read depth in some
21 regions (e.g. the chr1 centromere).
23 * Optionally write per-sample read depth and per-sample strand bias
26 * Compute equal-tail (Bayesian) credible interval of site allele
27 frequency at the CI95 VCF annotation.
29 * Merged the vcfutils.pl varFilter and filter4vcf for better SNP/indel
32 (0.1.10: 16 November 2010, r829)
36 Beta Release 0.1.9 (27 October, 2010)
37 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 This release is featured as the first major improvement to the samtools'
40 SNP caller. It comes with a revised MAQ error model, the support of
41 multi-sample SNP calling and the computation of base alignment quality
44 The revised MAQ error model is based on the original model. It solves an
45 issue of miscalling SNPs in repetitive regions. Althought such SNPs can
46 usually be filtered at a later step, they mess up unfiltered calls. This
47 is a theoretical flaw in the original model. The revised MAQ model
48 deprecates the orginal MAQ model and the simplified SOAPsnp model.
50 Multi-sample SNP calling is separated in two steps. The first is done by
51 samtools mpileup and the second by a new program, bcftools, which is
52 included in the samtools source code tree. Multi-sample SNP calling also
53 works for single sample and has the advantage of enabling more powerful
54 filtration. It is likely to deprecate pileup in future once a proper
55 indel calling method is implemented.
57 BAQ is the Phred-scaled probability of a read base being wrongly
58 aligned. Capping base quality by BAQ has been shown to be very effective
59 in suppressing false SNPs caused by misalignments around indels or in
60 low-complexity regions with acceptable compromise on computation
61 time. This strategy is highly recommended and can be used with other SNP
64 In addition to the three major improvements, other notable changes are:
66 * Changes to the pileup format. A reference skip (the N CIGAR operator)
67 is shown as '<' or '>' depending on the strand. Tview is also changed
70 * Accelerated pileup. The plain pileup is about 50% faster.
72 * Regional merge. The merge command now accepts a new option to merge
73 files in a specified region.
75 * Fixed a bug in bgzip and razip which causes source files to be
76 deleted even if option -c is applied.
78 * In APIs, propogate errors to downstream callers and make samtools
79 return non-zero values once errors occur.
81 (0.1.9: 27 October 2010, r783)
85 Beta Release 0.1.8 (11 July, 2010)
86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
88 Notable functional changes:
90 * Added the `reheader' command which replaces a BAM header with a new
91 header. This command is much faster than replacing header by
92 BAM->SAM->BAM conversions.
94 * Added the `mpileup' command which computes the pileup of multiple
97 * The `index' command now stores the number of mapped and unmapped
98 reads in the index file. This information can be retrieved quickly by
99 the new `idxstats' command.
101 * By default, pileup used the SOAPsnp model for SNP calling. This
102 avoids the floating overflow in the MAQ model which leads to spurious
103 calls in repetitive regions, although these calls will be immediately
104 filtered by varFilter.
106 * The `tview' command now correctly handles CIGARs like 7I10M and
107 10M1P1I10M which cause assertion failure in earlier versions.
109 * Tview accepts a region like `=10,000' where `=' stands for the
110 current sequence name. This saves typing for long sequence names.
112 * Added the `-d' option to `pileup' which avoids slow indel calling
113 in ultradeep regions by subsampling reads locally.
115 * Added the `-R' option to `view' which retrieves alignments in read
116 groups listed in the specified file.
118 Performance improvements:
120 * The BAM->SAM conversion is up to twice faster, depending on the
121 characteristic of the input.
123 * Parsing SAM headers with a lot of reference sequences is now much
126 * The number of lseek() calls per query is reduced when the query
127 region contains no read alignments.
131 * Fixed an issue in the indel caller that leads to miscall of indels.
132 Note that this solution may not work well when the sequencing indel
133 error rate is higher than the rate of SNPs.
135 * Fixed another issue in the indel caller which may lead to incorrect
138 * Fixed a bug in `sort' when option `-o' is applied.
140 * Fixed a bug in `view -r'.
142 APIs and other changes:
144 * Added iterator interfaces to random access and pileup. The callback
145 interfaces directly call the iterator interfaces.
147 * The BGZF blocks holding the BAM header are indepedent of alignment
148 BGZF blocks. Alignment records shorter than 64kB is guaranteed to be
149 fully contained in one BGZF block. This change is fully compatible
150 with the old version of samtools/picard.
152 Changes in other utilities:
154 * Updated export2sam.pl by Chris Saunders.
156 * Improved the sam2vcf.pl script.
158 * Added a Python version of varfilter.py by Aylwyn Scally.
160 (0.1.8: 11 July 2010, r613)
164 Beta Release 0.1.7 (10 November, 2009)
165 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
169 * Improved the indel caller in complex scenariors, in particular for
170 long reads. The indel caller is now able to make reasonable indel
171 calls from Craig Venter capillary reads.
173 * Rewrote single-end duplicate removal with improved
174 performance. Paired-end reads are not touched.
176 * Duplicate removal is now library aware. Samtools remove potential
177 PCR/optical dupliates inside a library rather than across libraries.
179 * SAM header is now fully parsed, although this functionality is not
180 used in merging and so on.
182 * In samtools merge, optionally take the input file name as RG-ID and
183 attach the RG tag to each alignment.
185 * Added FTP support in the RAZF library. RAZF-compressed reference
186 sequence can be retrieved remotely.
188 * Improved network support for Win32.
190 * Samtools sort and merge are now stable.
192 Changes in other utilities:
194 * Implemented sam2vcf.pl that converts the pileup format to the VCF
197 * This release of samtools is known to work with the latest
198 Bio-Samtools Perl module.
200 (0.1.7: 10 November 2009, r510)
204 Beta Release 0.1.6 (2 September, 2009)
205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
209 * In tview, do not show a blank screen when no reads mapped to the
210 corresponding region.
212 * Implemented native HTTP support in the BGZF library. Samtools is now
213 able to directly open a BAM file on HTTP. HTTP proxy is also
214 supported via the "http_proxy" environmental variable.
216 * Samtools is now compitable with the MinGW (win32) compiler and the
219 * The calmd (or fillmd) command now calculates the NM tag and replaces
220 MD tags if they are wrong.
222 * The view command now recognizes and optionally prints FLAG in HEXs or
223 strings to make a SAM file more friendly to human eyes. This is a
224 samtools-C extension, not implemented in Picard for the time
225 being. Please type `samtools view -?' for more information.
227 * BAM files now have an end-of-file (EOF) marker to facilitate
228 truncation detection. A warning will be given if an on-disk BAM file
229 does not have this marker. The warning will be seen on BAM files
230 generated by an older version of samtools. It does NO harm.
232 * New key bindings in tview: `r' to show read names and `s' to show
233 reference skip (N operation) as deletions.
235 * Fixed a bug in `samtools merge -n'.
237 * Samtools merge now optionally copies the header of a user specified
238 SAM file to the resultant BAM output.
240 * Samtools pileup/tview works with a CIGAR with the first or the last
241 operation is an indel.
243 * Fixed a bug in bam_aux_get().
246 Changes in other utilies:
248 * Fixed wrong FLAG in maq2sam.
251 (0.1.6: 2 September 2009, r453)
255 Beta Release 0.1.5 (7 July, 2009)
256 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
260 * Support opening a BAM alignment on FTP. Users can now use "tview" to
261 view alignments at the NCBI ftp site. Please read manual for more
264 * In library, propagate errors rather than exit or complain assertion
267 * Simplified the building system and fixed compiling errors caused by
270 * Fixed an issue about lost header information when a SAM is imported
273 * Implemented "samtool.pl varFilter" which filters both SNPs and short
274 indels. This command replaces "indelFilter".
276 * Implemented "samtools.pl pileup2fq" to generate FASTQ consensus from
279 * In pileup, cap mapping quality at 60. This helps filtering when
280 different aligners are in use.
282 * In pileup, allow to output variant sites only.
284 * Made pileup generate correct calls in repetitive region. At the same
285 time, I am considering to implement a simplified model in SOAPsnp,
286 although this has not happened yet.
288 * In view, added '-u' option to output BAM without compression. This
289 option is preferred when the output is piped to other commands.
291 * In view, added '-l' and '-r' to get the alignments for one library or
292 read group. The "@RG" header lines are now partially parsed.
294 * Do not include command line utilities to libbam.a.
296 * Fixed memory leaks in pileup and bam_view1().
298 * Made faidx more tolerant to empty lines right before or after FASTA >
302 Changes in other utilities:
304 * Updated novo2sam.pl by Colin Hercus, the key developer of novoalign.
307 This release involves several modifications to the key code base which
308 may potentially introduce new bugs even though we have tried to minimize
309 this by testing on several examples. Please let us know if you catch
312 (0.1.5: 7 July 2009, r373)
316 Beta Release 0.1.4 (21 May, 2009)
317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
321 * Added the 'rmdupse' command: removing duplicates for SE reads.
323 * Fixed a critical bug in the indel caller: clipped alignments are not
326 * Fixed a bug in the tview: gapped alignment may be incorrectly
329 * Unified the interface to BAM and SAM I/O. This is done by
330 implementing a wrapper on top of the old APIs and therefore old APIs
331 are still valid. The new I/O APIs also recognize the @SQ header
334 * Generate the MD tag.
336 * Generate "=" bases. However, the indel caller will not work when "="
339 * Enhanced support of color-read display (by Nils Homer).
341 * Implemented the GNU building system. However, currently the building
342 system does not generate libbam.a. We will improve this later. For
343 the time being, `make -f Makefile.generic' is preferred.
345 * Fixed a minor bug in pileup: the first read in a chromosome may be
348 * Fixed bugs in bam_aux.c. These bugs do not affect other components as
349 they were not used previously.
351 * Output the 'SM' tag from maq2sam.
353 (0.1.4: 21 May 2009, r297)
357 Beta Release 0.1.3 (15 April, 2009)
358 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
360 Notable changes in SAMtools:
362 * SAMtools is more consistent with the specification: a) '*' in the
363 QUAL field is allowed; b) the field separator is TAB only and SPACE
364 is treated as a character in a field; c) empty header is allowed.
366 * Implemented GLFv3 support in pileup.
368 * Fixed a severe bug in fixmate: strand information is wrongly
371 * Fixed a bug in alignment retrieval: alignments bridging n*16384bp are
372 not correctly retrieved sometimes.
374 * Fixed a bug in rmdup: segfault if unmapped reads are present.
376 * Move indel_filter.pl to samtools.pl and improved the filtering by
377 checking the actual number of alignments containing indels. The indel
378 pileup line is also changed a little to make this filtration easier.
380 * Fixed a minor bug in indexing: the bin number of an unmapped read is
383 * Added `flagstat' command to show statistics on the FLAG field.
385 * Improved indel caller by setting the maximum window size in local
388 Changes in other utilities:
390 * Fixed a bug in maq2sam: a tag name is obsolete.
392 * Improvement to wgsim: a) added support for SOLiD read simulation; b)
393 show the number of substitutions/indels/errors in read name; c)
394 considerable code clean up.
396 * Various converters: improved functionality in general.
398 * Updated the example SAM due to the previous bug in fixmate.
400 (0.1.3: 15 April 2009, r227)
404 Beta Release 0.1.2 (28 January, 2008)
405 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
407 Notable changes in SAMtools:
409 * Implemented a Bayesian indel caller. The new caller generate scores
410 and genotype and is potentially more accurate than Maq's indel
411 caller. The pileup format is also changed accordingly.
413 * Implemented rmdup command: remove potential PCR duplicates. Note that
414 this command ONLY works for FR orientation and requires ISIZE is
417 * Added fixmate command: fill in mate coordinates, ISIZE and mate
418 related flags from a name-sorted alignment.
420 * Fixed a bug in indexing: reads bridging 16x kbp were not retrieved.
422 * Allow to select reads shown in the pileup output with a mask.
424 * Generate GLFv2 from pileup.
426 * Added two more flags for flagging PCR/optical duplicates and for QC
429 * Fixed a bug in sort command: name sorting for large alignment did not
432 * Allow to completely disable RAZF (using Makefile.lite) as some people
433 have problem to compile it.
435 * Fixed a bug in import command when there are reads without
438 * Fixed a bug in tview: clipping broke the alignment viewer.
440 * Fixed a compiling error when _NO_CURSES is applied.
442 * Fixed a bug in merge command.
444 Changes in other utilities:
446 * Added wgsim, a paired-end reads simulator. Wgsim was adapted from
447 maq's reads simulator. Colin Hercus further improved it to allow
450 * Added wgsim_eval.pl, a script that evaluates the accuracy of
451 alignment on reads generated by wgsim.
453 * Added soap2sam.pl, a SOAP2->SAM converter. This converter does not
454 work properly when multiple hits are output.
456 * Added bowtie2sam.pl, a Bowtie->SAM converter. Only the top hit will
457 be retained when multiple hits are present.
459 * Fixed a bug in export2sam.pl for QC reads.
461 * Support RG tag at MAQ->SAM converter.
463 * Added novo2sam.pl, a NovoAlign->SAM converter. Multiple hits and
464 indel are not properly handled, though.
466 * Added zoom2sam.pl, a ZOOM->SAM converter. It only works with the
467 default Illumina output.
469 (0.1.2: 28 January 2008; r116)
473 Beta Release 0.1.1 (22 December, 2008)
474 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
476 The is the first public release of samtools. For more information,
477 please check the manual page `samtools.1' and the samtools website
478 http://samtools.sourceforge.net