1 Beta release 0.1.11 (21 November, 2010)
2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
4 This is mainly a bug fix release:
6 * Fixed a bug in random retrieval (since 0.1.8). It occurs when reads
7 are retrieved from a small region containing no reads.
9 * Fixed a bug in pileup (since 0.1.9). The bug causes an assertion
10 failure when the first CIGAR operation is a deletion.
12 * Improved fault tolerence in remote access.
14 One minor feature has been implemented in bcftools:
16 * Added a reference-free variant calling mode. In this mode, a site is
17 regarded as a variat iff the sample(s) contains two or more alleles;
18 the meaning of the QUAL field in the VCF output is changed
19 accordingly. Effectively, the reference allele is irrelevant to the
20 result in the new mode, although the reference sequence has to be
21 used in realignment when SAMtools computes genotype likelihoods.
23 In addition, since 0.1.10, the `pileup' command has been deprecated by
24 `mpileup' which is more powerful and more accurate. The `pileup' command
25 will not be removed in the next few releases, but new features will not
28 (0.1.11: 21 November 2010, r851)
32 Beta Release 0.1.10 (16 November, 2010)
33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
35 This release is featured as the first major improvement to the indel
36 caller. The method is similar to the old one implemented in the pileup
37 command, but the details are handled more carefully both in theory and
38 in practice. As a result, the new indel caller usually gives more
39 accurate indel calls, though at the cost of sensitivity. The caller is
40 implemented in the mpileup command and is invoked by default. It works
41 with multiple samples.
43 Other notable changes:
45 * With the -r option, the calmd command writes the difference between
46 the original base quality and the BAQ capped base quality at the BQ
47 tag but does not modify the base quality. Please use -Ar to overwrite
48 the original base quality (the 0.1.9 behavior).
50 * Allow to set a maximum per-sample read depth to reduce memory. In
51 0.1.9, most of memory is wasted for the ultra high read depth in some
52 regions (e.g. the chr1 centromere).
54 * Optionally write per-sample read depth and per-sample strand bias
57 * Compute equal-tail (Bayesian) credible interval of site allele
58 frequency at the CI95 VCF annotation.
60 * Merged the vcfutils.pl varFilter and filter4vcf for better SNP/indel
63 (0.1.10: 16 November 2010, r829)
67 Beta Release 0.1.9 (27 October, 2010)
68 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
70 This release is featured as the first major improvement to the samtools'
71 SNP caller. It comes with a revised MAQ error model, the support of
72 multi-sample SNP calling and the computation of base alignment quality
75 The revised MAQ error model is based on the original model. It solves an
76 issue of miscalling SNPs in repetitive regions. Althought such SNPs can
77 usually be filtered at a later step, they mess up unfiltered calls. This
78 is a theoretical flaw in the original model. The revised MAQ model
79 deprecates the orginal MAQ model and the simplified SOAPsnp model.
81 Multi-sample SNP calling is separated in two steps. The first is done by
82 samtools mpileup and the second by a new program, bcftools, which is
83 included in the samtools source code tree. Multi-sample SNP calling also
84 works for single sample and has the advantage of enabling more powerful
85 filtration. It is likely to deprecate pileup in future once a proper
86 indel calling method is implemented.
88 BAQ is the Phred-scaled probability of a read base being wrongly
89 aligned. Capping base quality by BAQ has been shown to be very effective
90 in suppressing false SNPs caused by misalignments around indels or in
91 low-complexity regions with acceptable compromise on computation
92 time. This strategy is highly recommended and can be used with other SNP
95 In addition to the three major improvements, other notable changes are:
97 * Changes to the pileup format. A reference skip (the N CIGAR operator)
98 is shown as '<' or '>' depending on the strand. Tview is also changed
101 * Accelerated pileup. The plain pileup is about 50% faster.
103 * Regional merge. The merge command now accepts a new option to merge
104 files in a specified region.
106 * Fixed a bug in bgzip and razip which causes source files to be
107 deleted even if option -c is applied.
109 * In APIs, propogate errors to downstream callers and make samtools
110 return non-zero values once errors occur.
112 (0.1.9: 27 October 2010, r783)
116 Beta Release 0.1.8 (11 July, 2010)
117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
119 Notable functional changes:
121 * Added the `reheader' command which replaces a BAM header with a new
122 header. This command is much faster than replacing header by
123 BAM->SAM->BAM conversions.
125 * Added the `mpileup' command which computes the pileup of multiple
128 * The `index' command now stores the number of mapped and unmapped
129 reads in the index file. This information can be retrieved quickly by
130 the new `idxstats' command.
132 * By default, pileup used the SOAPsnp model for SNP calling. This
133 avoids the floating overflow in the MAQ model which leads to spurious
134 calls in repetitive regions, although these calls will be immediately
135 filtered by varFilter.
137 * The `tview' command now correctly handles CIGARs like 7I10M and
138 10M1P1I10M which cause assertion failure in earlier versions.
140 * Tview accepts a region like `=10,000' where `=' stands for the
141 current sequence name. This saves typing for long sequence names.
143 * Added the `-d' option to `pileup' which avoids slow indel calling
144 in ultradeep regions by subsampling reads locally.
146 * Added the `-R' option to `view' which retrieves alignments in read
147 groups listed in the specified file.
149 Performance improvements:
151 * The BAM->SAM conversion is up to twice faster, depending on the
152 characteristic of the input.
154 * Parsing SAM headers with a lot of reference sequences is now much
157 * The number of lseek() calls per query is reduced when the query
158 region contains no read alignments.
162 * Fixed an issue in the indel caller that leads to miscall of indels.
163 Note that this solution may not work well when the sequencing indel
164 error rate is higher than the rate of SNPs.
166 * Fixed another issue in the indel caller which may lead to incorrect
169 * Fixed a bug in `sort' when option `-o' is applied.
171 * Fixed a bug in `view -r'.
173 APIs and other changes:
175 * Added iterator interfaces to random access and pileup. The callback
176 interfaces directly call the iterator interfaces.
178 * The BGZF blocks holding the BAM header are indepedent of alignment
179 BGZF blocks. Alignment records shorter than 64kB is guaranteed to be
180 fully contained in one BGZF block. This change is fully compatible
181 with the old version of samtools/picard.
183 Changes in other utilities:
185 * Updated export2sam.pl by Chris Saunders.
187 * Improved the sam2vcf.pl script.
189 * Added a Python version of varfilter.py by Aylwyn Scally.
191 (0.1.8: 11 July 2010, r613)
195 Beta Release 0.1.7 (10 November, 2009)
196 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 * Improved the indel caller in complex scenariors, in particular for
201 long reads. The indel caller is now able to make reasonable indel
202 calls from Craig Venter capillary reads.
204 * Rewrote single-end duplicate removal with improved
205 performance. Paired-end reads are not touched.
207 * Duplicate removal is now library aware. Samtools remove potential
208 PCR/optical dupliates inside a library rather than across libraries.
210 * SAM header is now fully parsed, although this functionality is not
211 used in merging and so on.
213 * In samtools merge, optionally take the input file name as RG-ID and
214 attach the RG tag to each alignment.
216 * Added FTP support in the RAZF library. RAZF-compressed reference
217 sequence can be retrieved remotely.
219 * Improved network support for Win32.
221 * Samtools sort and merge are now stable.
223 Changes in other utilities:
225 * Implemented sam2vcf.pl that converts the pileup format to the VCF
228 * This release of samtools is known to work with the latest
229 Bio-Samtools Perl module.
231 (0.1.7: 10 November 2009, r510)
235 Beta Release 0.1.6 (2 September, 2009)
236 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
240 * In tview, do not show a blank screen when no reads mapped to the
241 corresponding region.
243 * Implemented native HTTP support in the BGZF library. Samtools is now
244 able to directly open a BAM file on HTTP. HTTP proxy is also
245 supported via the "http_proxy" environmental variable.
247 * Samtools is now compitable with the MinGW (win32) compiler and the
250 * The calmd (or fillmd) command now calculates the NM tag and replaces
251 MD tags if they are wrong.
253 * The view command now recognizes and optionally prints FLAG in HEXs or
254 strings to make a SAM file more friendly to human eyes. This is a
255 samtools-C extension, not implemented in Picard for the time
256 being. Please type `samtools view -?' for more information.
258 * BAM files now have an end-of-file (EOF) marker to facilitate
259 truncation detection. A warning will be given if an on-disk BAM file
260 does not have this marker. The warning will be seen on BAM files
261 generated by an older version of samtools. It does NO harm.
263 * New key bindings in tview: `r' to show read names and `s' to show
264 reference skip (N operation) as deletions.
266 * Fixed a bug in `samtools merge -n'.
268 * Samtools merge now optionally copies the header of a user specified
269 SAM file to the resultant BAM output.
271 * Samtools pileup/tview works with a CIGAR with the first or the last
272 operation is an indel.
274 * Fixed a bug in bam_aux_get().
277 Changes in other utilies:
279 * Fixed wrong FLAG in maq2sam.
282 (0.1.6: 2 September 2009, r453)
286 Beta Release 0.1.5 (7 July, 2009)
287 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
291 * Support opening a BAM alignment on FTP. Users can now use "tview" to
292 view alignments at the NCBI ftp site. Please read manual for more
295 * In library, propagate errors rather than exit or complain assertion
298 * Simplified the building system and fixed compiling errors caused by
301 * Fixed an issue about lost header information when a SAM is imported
304 * Implemented "samtool.pl varFilter" which filters both SNPs and short
305 indels. This command replaces "indelFilter".
307 * Implemented "samtools.pl pileup2fq" to generate FASTQ consensus from
310 * In pileup, cap mapping quality at 60. This helps filtering when
311 different aligners are in use.
313 * In pileup, allow to output variant sites only.
315 * Made pileup generate correct calls in repetitive region. At the same
316 time, I am considering to implement a simplified model in SOAPsnp,
317 although this has not happened yet.
319 * In view, added '-u' option to output BAM without compression. This
320 option is preferred when the output is piped to other commands.
322 * In view, added '-l' and '-r' to get the alignments for one library or
323 read group. The "@RG" header lines are now partially parsed.
325 * Do not include command line utilities to libbam.a.
327 * Fixed memory leaks in pileup and bam_view1().
329 * Made faidx more tolerant to empty lines right before or after FASTA >
333 Changes in other utilities:
335 * Updated novo2sam.pl by Colin Hercus, the key developer of novoalign.
338 This release involves several modifications to the key code base which
339 may potentially introduce new bugs even though we have tried to minimize
340 this by testing on several examples. Please let us know if you catch
343 (0.1.5: 7 July 2009, r373)
347 Beta Release 0.1.4 (21 May, 2009)
348 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
352 * Added the 'rmdupse' command: removing duplicates for SE reads.
354 * Fixed a critical bug in the indel caller: clipped alignments are not
357 * Fixed a bug in the tview: gapped alignment may be incorrectly
360 * Unified the interface to BAM and SAM I/O. This is done by
361 implementing a wrapper on top of the old APIs and therefore old APIs
362 are still valid. The new I/O APIs also recognize the @SQ header
365 * Generate the MD tag.
367 * Generate "=" bases. However, the indel caller will not work when "="
370 * Enhanced support of color-read display (by Nils Homer).
372 * Implemented the GNU building system. However, currently the building
373 system does not generate libbam.a. We will improve this later. For
374 the time being, `make -f Makefile.generic' is preferred.
376 * Fixed a minor bug in pileup: the first read in a chromosome may be
379 * Fixed bugs in bam_aux.c. These bugs do not affect other components as
380 they were not used previously.
382 * Output the 'SM' tag from maq2sam.
384 (0.1.4: 21 May 2009, r297)
388 Beta Release 0.1.3 (15 April, 2009)
389 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
391 Notable changes in SAMtools:
393 * SAMtools is more consistent with the specification: a) '*' in the
394 QUAL field is allowed; b) the field separator is TAB only and SPACE
395 is treated as a character in a field; c) empty header is allowed.
397 * Implemented GLFv3 support in pileup.
399 * Fixed a severe bug in fixmate: strand information is wrongly
402 * Fixed a bug in alignment retrieval: alignments bridging n*16384bp are
403 not correctly retrieved sometimes.
405 * Fixed a bug in rmdup: segfault if unmapped reads are present.
407 * Move indel_filter.pl to samtools.pl and improved the filtering by
408 checking the actual number of alignments containing indels. The indel
409 pileup line is also changed a little to make this filtration easier.
411 * Fixed a minor bug in indexing: the bin number of an unmapped read is
414 * Added `flagstat' command to show statistics on the FLAG field.
416 * Improved indel caller by setting the maximum window size in local
419 Changes in other utilities:
421 * Fixed a bug in maq2sam: a tag name is obsolete.
423 * Improvement to wgsim: a) added support for SOLiD read simulation; b)
424 show the number of substitutions/indels/errors in read name; c)
425 considerable code clean up.
427 * Various converters: improved functionality in general.
429 * Updated the example SAM due to the previous bug in fixmate.
431 (0.1.3: 15 April 2009, r227)
435 Beta Release 0.1.2 (28 January, 2008)
436 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
438 Notable changes in SAMtools:
440 * Implemented a Bayesian indel caller. The new caller generate scores
441 and genotype and is potentially more accurate than Maq's indel
442 caller. The pileup format is also changed accordingly.
444 * Implemented rmdup command: remove potential PCR duplicates. Note that
445 this command ONLY works for FR orientation and requires ISIZE is
448 * Added fixmate command: fill in mate coordinates, ISIZE and mate
449 related flags from a name-sorted alignment.
451 * Fixed a bug in indexing: reads bridging 16x kbp were not retrieved.
453 * Allow to select reads shown in the pileup output with a mask.
455 * Generate GLFv2 from pileup.
457 * Added two more flags for flagging PCR/optical duplicates and for QC
460 * Fixed a bug in sort command: name sorting for large alignment did not
463 * Allow to completely disable RAZF (using Makefile.lite) as some people
464 have problem to compile it.
466 * Fixed a bug in import command when there are reads without
469 * Fixed a bug in tview: clipping broke the alignment viewer.
471 * Fixed a compiling error when _NO_CURSES is applied.
473 * Fixed a bug in merge command.
475 Changes in other utilities:
477 * Added wgsim, a paired-end reads simulator. Wgsim was adapted from
478 maq's reads simulator. Colin Hercus further improved it to allow
481 * Added wgsim_eval.pl, a script that evaluates the accuracy of
482 alignment on reads generated by wgsim.
484 * Added soap2sam.pl, a SOAP2->SAM converter. This converter does not
485 work properly when multiple hits are output.
487 * Added bowtie2sam.pl, a Bowtie->SAM converter. Only the top hit will
488 be retained when multiple hits are present.
490 * Fixed a bug in export2sam.pl for QC reads.
492 * Support RG tag at MAQ->SAM converter.
494 * Added novo2sam.pl, a NovoAlign->SAM converter. Multiple hits and
495 indel are not properly handled, though.
497 * Added zoom2sam.pl, a ZOOM->SAM converter. It only works with the
498 default Illumina output.
500 (0.1.2: 28 January 2008; r116)
504 Beta Release 0.1.1 (22 December, 2008)
505 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
507 The is the first public release of samtools. For more information,
508 please check the manual page `samtools.1' and the samtools website
509 http://samtools.sourceforge.net