1 Beta release 0.1.12 (2 December, 2010)
2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
4 This is another bug fix release:
6 * Fixed a memory violation in mpileup, which causes segfault. Release
7 0.1.9 and above are affected.
9 * Fixed a memory violation in the indel caller, which does not causes
10 segfault, but may potentially affect deletion calls in an unexpected
11 way. Release 0.1.10 and above are affected.
13 * Fixed a bug in computing r-square in bcftools. Few are using this
14 functionality and it only has minor effect.
16 * Fixed a memory leak in bam_fetch().
18 * Fixed a bug in writing meta information to the BAM index for the last
19 sequence. This bug is invisible to most users, but it is a bug anyway.
21 (0.1.12: 2 December 2010, r859)
25 Beta release 0.1.11 (21 November, 2010)
26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
28 This is mainly a bug fix release:
30 * Fixed a bug in random retrieval (since 0.1.8). It occurs when reads
31 are retrieved from a small region containing no reads.
33 * Fixed a bug in pileup (since 0.1.9). The bug causes an assertion
34 failure when the first CIGAR operation is a deletion.
36 * Improved fault tolerence in remote access.
38 One minor feature has been implemented in bcftools:
40 * Added a reference-free variant calling mode. In this mode, a site is
41 regarded as a variat iff the sample(s) contains two or more alleles;
42 the meaning of the QUAL field in the VCF output is changed
43 accordingly. Effectively, the reference allele is irrelevant to the
44 result in the new mode, although the reference sequence has to be
45 used in realignment when SAMtools computes genotype likelihoods.
47 In addition, since 0.1.10, the `pileup' command has been deprecated by
48 `mpileup' which is more powerful and more accurate. The `pileup' command
49 will not be removed in the next few releases, but new features will not
52 (0.1.11: 21 November 2010, r851)
56 Beta Release 0.1.10 (16 November, 2010)
57 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
59 This release is featured as the first major improvement to the indel
60 caller. The method is similar to the old one implemented in the pileup
61 command, but the details are handled more carefully both in theory and
62 in practice. As a result, the new indel caller usually gives more
63 accurate indel calls, though at the cost of sensitivity. The caller is
64 implemented in the mpileup command and is invoked by default. It works
65 with multiple samples.
67 Other notable changes:
69 * With the -r option, the calmd command writes the difference between
70 the original base quality and the BAQ capped base quality at the BQ
71 tag but does not modify the base quality. Please use -Ar to overwrite
72 the original base quality (the 0.1.9 behavior).
74 * Allow to set a maximum per-sample read depth to reduce memory. In
75 0.1.9, most of memory is wasted for the ultra high read depth in some
76 regions (e.g. the chr1 centromere).
78 * Optionally write per-sample read depth and per-sample strand bias
81 * Compute equal-tail (Bayesian) credible interval of site allele
82 frequency at the CI95 VCF annotation.
84 * Merged the vcfutils.pl varFilter and filter4vcf for better SNP/indel
87 (0.1.10: 16 November 2010, r829)
91 Beta Release 0.1.9 (27 October, 2010)
92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
94 This release is featured as the first major improvement to the samtools'
95 SNP caller. It comes with a revised MAQ error model, the support of
96 multi-sample SNP calling and the computation of base alignment quality
99 The revised MAQ error model is based on the original model. It solves an
100 issue of miscalling SNPs in repetitive regions. Althought such SNPs can
101 usually be filtered at a later step, they mess up unfiltered calls. This
102 is a theoretical flaw in the original model. The revised MAQ model
103 deprecates the orginal MAQ model and the simplified SOAPsnp model.
105 Multi-sample SNP calling is separated in two steps. The first is done by
106 samtools mpileup and the second by a new program, bcftools, which is
107 included in the samtools source code tree. Multi-sample SNP calling also
108 works for single sample and has the advantage of enabling more powerful
109 filtration. It is likely to deprecate pileup in future once a proper
110 indel calling method is implemented.
112 BAQ is the Phred-scaled probability of a read base being wrongly
113 aligned. Capping base quality by BAQ has been shown to be very effective
114 in suppressing false SNPs caused by misalignments around indels or in
115 low-complexity regions with acceptable compromise on computation
116 time. This strategy is highly recommended and can be used with other SNP
119 In addition to the three major improvements, other notable changes are:
121 * Changes to the pileup format. A reference skip (the N CIGAR operator)
122 is shown as '<' or '>' depending on the strand. Tview is also changed
125 * Accelerated pileup. The plain pileup is about 50% faster.
127 * Regional merge. The merge command now accepts a new option to merge
128 files in a specified region.
130 * Fixed a bug in bgzip and razip which causes source files to be
131 deleted even if option -c is applied.
133 * In APIs, propogate errors to downstream callers and make samtools
134 return non-zero values once errors occur.
136 (0.1.9: 27 October 2010, r783)
140 Beta Release 0.1.8 (11 July, 2010)
141 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
143 Notable functional changes:
145 * Added the `reheader' command which replaces a BAM header with a new
146 header. This command is much faster than replacing header by
147 BAM->SAM->BAM conversions.
149 * Added the `mpileup' command which computes the pileup of multiple
152 * The `index' command now stores the number of mapped and unmapped
153 reads in the index file. This information can be retrieved quickly by
154 the new `idxstats' command.
156 * By default, pileup used the SOAPsnp model for SNP calling. This
157 avoids the floating overflow in the MAQ model which leads to spurious
158 calls in repetitive regions, although these calls will be immediately
159 filtered by varFilter.
161 * The `tview' command now correctly handles CIGARs like 7I10M and
162 10M1P1I10M which cause assertion failure in earlier versions.
164 * Tview accepts a region like `=10,000' where `=' stands for the
165 current sequence name. This saves typing for long sequence names.
167 * Added the `-d' option to `pileup' which avoids slow indel calling
168 in ultradeep regions by subsampling reads locally.
170 * Added the `-R' option to `view' which retrieves alignments in read
171 groups listed in the specified file.
173 Performance improvements:
175 * The BAM->SAM conversion is up to twice faster, depending on the
176 characteristic of the input.
178 * Parsing SAM headers with a lot of reference sequences is now much
181 * The number of lseek() calls per query is reduced when the query
182 region contains no read alignments.
186 * Fixed an issue in the indel caller that leads to miscall of indels.
187 Note that this solution may not work well when the sequencing indel
188 error rate is higher than the rate of SNPs.
190 * Fixed another issue in the indel caller which may lead to incorrect
193 * Fixed a bug in `sort' when option `-o' is applied.
195 * Fixed a bug in `view -r'.
197 APIs and other changes:
199 * Added iterator interfaces to random access and pileup. The callback
200 interfaces directly call the iterator interfaces.
202 * The BGZF blocks holding the BAM header are indepedent of alignment
203 BGZF blocks. Alignment records shorter than 64kB is guaranteed to be
204 fully contained in one BGZF block. This change is fully compatible
205 with the old version of samtools/picard.
207 Changes in other utilities:
209 * Updated export2sam.pl by Chris Saunders.
211 * Improved the sam2vcf.pl script.
213 * Added a Python version of varfilter.py by Aylwyn Scally.
215 (0.1.8: 11 July 2010, r613)
219 Beta Release 0.1.7 (10 November, 2009)
220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 * Improved the indel caller in complex scenariors, in particular for
225 long reads. The indel caller is now able to make reasonable indel
226 calls from Craig Venter capillary reads.
228 * Rewrote single-end duplicate removal with improved
229 performance. Paired-end reads are not touched.
231 * Duplicate removal is now library aware. Samtools remove potential
232 PCR/optical dupliates inside a library rather than across libraries.
234 * SAM header is now fully parsed, although this functionality is not
235 used in merging and so on.
237 * In samtools merge, optionally take the input file name as RG-ID and
238 attach the RG tag to each alignment.
240 * Added FTP support in the RAZF library. RAZF-compressed reference
241 sequence can be retrieved remotely.
243 * Improved network support for Win32.
245 * Samtools sort and merge are now stable.
247 Changes in other utilities:
249 * Implemented sam2vcf.pl that converts the pileup format to the VCF
252 * This release of samtools is known to work with the latest
253 Bio-Samtools Perl module.
255 (0.1.7: 10 November 2009, r510)
259 Beta Release 0.1.6 (2 September, 2009)
260 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
264 * In tview, do not show a blank screen when no reads mapped to the
265 corresponding region.
267 * Implemented native HTTP support in the BGZF library. Samtools is now
268 able to directly open a BAM file on HTTP. HTTP proxy is also
269 supported via the "http_proxy" environmental variable.
271 * Samtools is now compitable with the MinGW (win32) compiler and the
274 * The calmd (or fillmd) command now calculates the NM tag and replaces
275 MD tags if they are wrong.
277 * The view command now recognizes and optionally prints FLAG in HEXs or
278 strings to make a SAM file more friendly to human eyes. This is a
279 samtools-C extension, not implemented in Picard for the time
280 being. Please type `samtools view -?' for more information.
282 * BAM files now have an end-of-file (EOF) marker to facilitate
283 truncation detection. A warning will be given if an on-disk BAM file
284 does not have this marker. The warning will be seen on BAM files
285 generated by an older version of samtools. It does NO harm.
287 * New key bindings in tview: `r' to show read names and `s' to show
288 reference skip (N operation) as deletions.
290 * Fixed a bug in `samtools merge -n'.
292 * Samtools merge now optionally copies the header of a user specified
293 SAM file to the resultant BAM output.
295 * Samtools pileup/tview works with a CIGAR with the first or the last
296 operation is an indel.
298 * Fixed a bug in bam_aux_get().
301 Changes in other utilies:
303 * Fixed wrong FLAG in maq2sam.
306 (0.1.6: 2 September 2009, r453)
310 Beta Release 0.1.5 (7 July, 2009)
311 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
315 * Support opening a BAM alignment on FTP. Users can now use "tview" to
316 view alignments at the NCBI ftp site. Please read manual for more
319 * In library, propagate errors rather than exit or complain assertion
322 * Simplified the building system and fixed compiling errors caused by
325 * Fixed an issue about lost header information when a SAM is imported
328 * Implemented "samtool.pl varFilter" which filters both SNPs and short
329 indels. This command replaces "indelFilter".
331 * Implemented "samtools.pl pileup2fq" to generate FASTQ consensus from
334 * In pileup, cap mapping quality at 60. This helps filtering when
335 different aligners are in use.
337 * In pileup, allow to output variant sites only.
339 * Made pileup generate correct calls in repetitive region. At the same
340 time, I am considering to implement a simplified model in SOAPsnp,
341 although this has not happened yet.
343 * In view, added '-u' option to output BAM without compression. This
344 option is preferred when the output is piped to other commands.
346 * In view, added '-l' and '-r' to get the alignments for one library or
347 read group. The "@RG" header lines are now partially parsed.
349 * Do not include command line utilities to libbam.a.
351 * Fixed memory leaks in pileup and bam_view1().
353 * Made faidx more tolerant to empty lines right before or after FASTA >
357 Changes in other utilities:
359 * Updated novo2sam.pl by Colin Hercus, the key developer of novoalign.
362 This release involves several modifications to the key code base which
363 may potentially introduce new bugs even though we have tried to minimize
364 this by testing on several examples. Please let us know if you catch
367 (0.1.5: 7 July 2009, r373)
371 Beta Release 0.1.4 (21 May, 2009)
372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
376 * Added the 'rmdupse' command: removing duplicates for SE reads.
378 * Fixed a critical bug in the indel caller: clipped alignments are not
381 * Fixed a bug in the tview: gapped alignment may be incorrectly
384 * Unified the interface to BAM and SAM I/O. This is done by
385 implementing a wrapper on top of the old APIs and therefore old APIs
386 are still valid. The new I/O APIs also recognize the @SQ header
389 * Generate the MD tag.
391 * Generate "=" bases. However, the indel caller will not work when "="
394 * Enhanced support of color-read display (by Nils Homer).
396 * Implemented the GNU building system. However, currently the building
397 system does not generate libbam.a. We will improve this later. For
398 the time being, `make -f Makefile.generic' is preferred.
400 * Fixed a minor bug in pileup: the first read in a chromosome may be
403 * Fixed bugs in bam_aux.c. These bugs do not affect other components as
404 they were not used previously.
406 * Output the 'SM' tag from maq2sam.
408 (0.1.4: 21 May 2009, r297)
412 Beta Release 0.1.3 (15 April, 2009)
413 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
415 Notable changes in SAMtools:
417 * SAMtools is more consistent with the specification: a) '*' in the
418 QUAL field is allowed; b) the field separator is TAB only and SPACE
419 is treated as a character in a field; c) empty header is allowed.
421 * Implemented GLFv3 support in pileup.
423 * Fixed a severe bug in fixmate: strand information is wrongly
426 * Fixed a bug in alignment retrieval: alignments bridging n*16384bp are
427 not correctly retrieved sometimes.
429 * Fixed a bug in rmdup: segfault if unmapped reads are present.
431 * Move indel_filter.pl to samtools.pl and improved the filtering by
432 checking the actual number of alignments containing indels. The indel
433 pileup line is also changed a little to make this filtration easier.
435 * Fixed a minor bug in indexing: the bin number of an unmapped read is
438 * Added `flagstat' command to show statistics on the FLAG field.
440 * Improved indel caller by setting the maximum window size in local
443 Changes in other utilities:
445 * Fixed a bug in maq2sam: a tag name is obsolete.
447 * Improvement to wgsim: a) added support for SOLiD read simulation; b)
448 show the number of substitutions/indels/errors in read name; c)
449 considerable code clean up.
451 * Various converters: improved functionality in general.
453 * Updated the example SAM due to the previous bug in fixmate.
455 (0.1.3: 15 April 2009, r227)
459 Beta Release 0.1.2 (28 January, 2008)
460 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
462 Notable changes in SAMtools:
464 * Implemented a Bayesian indel caller. The new caller generate scores
465 and genotype and is potentially more accurate than Maq's indel
466 caller. The pileup format is also changed accordingly.
468 * Implemented rmdup command: remove potential PCR duplicates. Note that
469 this command ONLY works for FR orientation and requires ISIZE is
472 * Added fixmate command: fill in mate coordinates, ISIZE and mate
473 related flags from a name-sorted alignment.
475 * Fixed a bug in indexing: reads bridging 16x kbp were not retrieved.
477 * Allow to select reads shown in the pileup output with a mask.
479 * Generate GLFv2 from pileup.
481 * Added two more flags for flagging PCR/optical duplicates and for QC
484 * Fixed a bug in sort command: name sorting for large alignment did not
487 * Allow to completely disable RAZF (using Makefile.lite) as some people
488 have problem to compile it.
490 * Fixed a bug in import command when there are reads without
493 * Fixed a bug in tview: clipping broke the alignment viewer.
495 * Fixed a compiling error when _NO_CURSES is applied.
497 * Fixed a bug in merge command.
499 Changes in other utilities:
501 * Added wgsim, a paired-end reads simulator. Wgsim was adapted from
502 maq's reads simulator. Colin Hercus further improved it to allow
505 * Added wgsim_eval.pl, a script that evaluates the accuracy of
506 alignment on reads generated by wgsim.
508 * Added soap2sam.pl, a SOAP2->SAM converter. This converter does not
509 work properly when multiple hits are output.
511 * Added bowtie2sam.pl, a Bowtie->SAM converter. Only the top hit will
512 be retained when multiple hits are present.
514 * Fixed a bug in export2sam.pl for QC reads.
516 * Support RG tag at MAQ->SAM converter.
518 * Added novo2sam.pl, a NovoAlign->SAM converter. Multiple hits and
519 indel are not properly handled, though.
521 * Added zoom2sam.pl, a ZOOM->SAM converter. It only works with the
522 default Illumina output.
524 (0.1.2: 28 January 2008; r116)
528 Beta Release 0.1.1 (22 December, 2008)
529 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
531 The is the first public release of samtools. For more information,
532 please check the manual page `samtools.1' and the samtools website
533 http://samtools.sourceforge.net