1 Beta release 0.1.13 (1 March, 2011)
2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
4 The most important though largely invisible modification is the change of the
5 order of genotypes in the PL VCF/BCF tag. This is to conform the upcoming VCF
6 spec v4.1. The change means that 0.1.13 is not backward compatible with VCF/BCF
7 generated by samtools older than r921 inclusive. VCF/BCF generated by the new
8 samtools will contain a line `##fileformat=VCFv4.1' as well as the samtools
11 Single Individual Haplotyping (SIH) is added as an experimental feature. It
12 originally aims to produce haploid consensus from fosmid pool sequencing, but
13 also works with short-read data. For short reads, phased blocks are usually too
14 short to be useful in many applications, but they can help to rule out part of
15 SNPs close to INDELs or between copies of CNVs.
18 Other notable changes in samtools:
20 * Construct per-sample consensus to reduce the effect of nearby SNPs in INDEL
21 calling. This reduces the power but improves specificity.
23 * Improved sorting order checking in indexing. Now indexing is the preferred way
24 to check if a BAM is sorted.
26 * Added a switch `-E' to mpileup and calmd. This option uses an alternative way
27 to apply BAQ, which increases sensistivity, especially to MNPs, at the cost of
28 a little loss in specificity.
30 * Added `mpileup -A' to allow to use reads in anomalous pairs in SNP calling.
32 * Added `mpileup -m' to allow fine control of the collection of INDEL candidates.
34 * Added `mpileup -S' to compute per-sample strand bias P-value.
36 * Added `mpileup -G' to exclude read groups in variant calling.
38 * Fixed segfault in indel calling related to unmapped and refskip reads.
40 * Fixed an integer overflow in INDEL calling. This bug produces wrong INDEL
41 genotypes for longer short INDELs, typically over 10bp.
43 * Fixed a bug in tview on big-endian machines.
45 * Fixed a very rare memory issue in bam_md.c
47 * Fixed an out-of-boundary bug in mpileup when the read base is `N'.
49 * Fixed a compiling error when the knetfile library is not used. Fixed a
50 library compiling error due to the lack of bam_nt16_nt4_table[] table.
51 Suppress a compiling warning related to the latest zlib.
54 Other notable changes in bcftools:
56 * Updated the BCF spec.
58 * Added the `FQ' VCF INFO field, which gives the phred-scaled probability
59 of all samples being the samei (identical to the reference or all homozygous
60 variants). Option `view -f' has been dropped.
62 * Implementated of "vcfutils.pl vcf2fq" to generate a consensus sequence
63 similar to "samtools.pl pileup2fq".
65 * Make sure the GT FORMAT field is always the first FORMAT to conform the VCF
66 spec. Drop bcf-fix.pl.
68 * Output bcftools specific INFO and FORMAT in the VCF header.
70 * Added `view -s' to call variants from a subset of samples.
72 * Properly convert VCF to BCF with a user provided sequence dictionary. Nonetheless,
73 custom fields are still unparsed and will be stored as a missing value.
75 * Fixed a minor bug in Fisher's exact test; the results are rarely changed.
78 (0.1.13: 1 March 2011, r926:134)
82 Beta release 0.1.12a (2 December, 2010)
83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
85 This is another bug fix release:
87 * Fixed a memory violation in mpileup, which causes segfault. Release
88 0.1.9 and above are affected.
90 * Fixed a memory violation in the indel caller, which does not causes
91 segfault, but may potentially affect deletion calls in an unexpected
92 way. Release 0.1.10 and above are affected.
94 * Fixed a bug in computing r-square in bcftools. Few are using this
95 functionality and it only has minor effect.
97 * Fixed a memory leak in bam_fetch().
99 * Fixed a bug in writing meta information to the BAM index for the last
100 sequence. This bug is invisible to most users, but it is a bug anyway.
102 * Fixed a bug in bcftools which causes false "DP4=0,0,0,0" annotations.
104 (0.1.12: 2 December 2010, r862)
108 Beta release 0.1.11 (21 November, 2010)
109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
111 This is mainly a bug fix release:
113 * Fixed a bug in random retrieval (since 0.1.8). It occurs when reads
114 are retrieved from a small region containing no reads.
116 * Fixed a bug in pileup (since 0.1.9). The bug causes an assertion
117 failure when the first CIGAR operation is a deletion.
119 * Improved fault tolerence in remote access.
121 One minor feature has been implemented in bcftools:
123 * Added a reference-free variant calling mode. In this mode, a site is
124 regarded as a variat iff the sample(s) contains two or more alleles;
125 the meaning of the QUAL field in the VCF output is changed
126 accordingly. Effectively, the reference allele is irrelevant to the
127 result in the new mode, although the reference sequence has to be
128 used in realignment when SAMtools computes genotype likelihoods.
130 In addition, since 0.1.10, the `pileup' command has been deprecated by
131 `mpileup' which is more powerful and more accurate. The `pileup' command
132 will not be removed in the next few releases, but new features will not
135 (0.1.11: 21 November 2010, r851)
139 Beta Release 0.1.10 (16 November, 2010)
140 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
142 This release is featured as the first major improvement to the indel
143 caller. The method is similar to the old one implemented in the pileup
144 command, but the details are handled more carefully both in theory and
145 in practice. As a result, the new indel caller usually gives more
146 accurate indel calls, though at the cost of sensitivity. The caller is
147 implemented in the mpileup command and is invoked by default. It works
148 with multiple samples.
150 Other notable changes:
152 * With the -r option, the calmd command writes the difference between
153 the original base quality and the BAQ capped base quality at the BQ
154 tag but does not modify the base quality. Please use -Ar to overwrite
155 the original base quality (the 0.1.9 behavior).
157 * Allow to set a maximum per-sample read depth to reduce memory. In
158 0.1.9, most of memory is wasted for the ultra high read depth in some
159 regions (e.g. the chr1 centromere).
161 * Optionally write per-sample read depth and per-sample strand bias
164 * Compute equal-tail (Bayesian) credible interval of site allele
165 frequency at the CI95 VCF annotation.
167 * Merged the vcfutils.pl varFilter and filter4vcf for better SNP/indel
170 (0.1.10: 16 November 2010, r829)
174 Beta Release 0.1.9 (27 October, 2010)
175 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
177 This release is featured as the first major improvement to the samtools'
178 SNP caller. It comes with a revised MAQ error model, the support of
179 multi-sample SNP calling and the computation of base alignment quality
182 The revised MAQ error model is based on the original model. It solves an
183 issue of miscalling SNPs in repetitive regions. Althought such SNPs can
184 usually be filtered at a later step, they mess up unfiltered calls. This
185 is a theoretical flaw in the original model. The revised MAQ model
186 deprecates the orginal MAQ model and the simplified SOAPsnp model.
188 Multi-sample SNP calling is separated in two steps. The first is done by
189 samtools mpileup and the second by a new program, bcftools, which is
190 included in the samtools source code tree. Multi-sample SNP calling also
191 works for single sample and has the advantage of enabling more powerful
192 filtration. It is likely to deprecate pileup in future once a proper
193 indel calling method is implemented.
195 BAQ is the Phred-scaled probability of a read base being wrongly
196 aligned. Capping base quality by BAQ has been shown to be very effective
197 in suppressing false SNPs caused by misalignments around indels or in
198 low-complexity regions with acceptable compromise on computation
199 time. This strategy is highly recommended and can be used with other SNP
202 In addition to the three major improvements, other notable changes are:
204 * Changes to the pileup format. A reference skip (the N CIGAR operator)
205 is shown as '<' or '>' depending on the strand. Tview is also changed
208 * Accelerated pileup. The plain pileup is about 50% faster.
210 * Regional merge. The merge command now accepts a new option to merge
211 files in a specified region.
213 * Fixed a bug in bgzip and razip which causes source files to be
214 deleted even if option -c is applied.
216 * In APIs, propogate errors to downstream callers and make samtools
217 return non-zero values once errors occur.
219 (0.1.9: 27 October 2010, r783)
223 Beta Release 0.1.8 (11 July, 2010)
224 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
226 Notable functional changes:
228 * Added the `reheader' command which replaces a BAM header with a new
229 header. This command is much faster than replacing header by
230 BAM->SAM->BAM conversions.
232 * Added the `mpileup' command which computes the pileup of multiple
235 * The `index' command now stores the number of mapped and unmapped
236 reads in the index file. This information can be retrieved quickly by
237 the new `idxstats' command.
239 * By default, pileup used the SOAPsnp model for SNP calling. This
240 avoids the floating overflow in the MAQ model which leads to spurious
241 calls in repetitive regions, although these calls will be immediately
242 filtered by varFilter.
244 * The `tview' command now correctly handles CIGARs like 7I10M and
245 10M1P1I10M which cause assertion failure in earlier versions.
247 * Tview accepts a region like `=10,000' where `=' stands for the
248 current sequence name. This saves typing for long sequence names.
250 * Added the `-d' option to `pileup' which avoids slow indel calling
251 in ultradeep regions by subsampling reads locally.
253 * Added the `-R' option to `view' which retrieves alignments in read
254 groups listed in the specified file.
256 Performance improvements:
258 * The BAM->SAM conversion is up to twice faster, depending on the
259 characteristic of the input.
261 * Parsing SAM headers with a lot of reference sequences is now much
264 * The number of lseek() calls per query is reduced when the query
265 region contains no read alignments.
269 * Fixed an issue in the indel caller that leads to miscall of indels.
270 Note that this solution may not work well when the sequencing indel
271 error rate is higher than the rate of SNPs.
273 * Fixed another issue in the indel caller which may lead to incorrect
276 * Fixed a bug in `sort' when option `-o' is applied.
278 * Fixed a bug in `view -r'.
280 APIs and other changes:
282 * Added iterator interfaces to random access and pileup. The callback
283 interfaces directly call the iterator interfaces.
285 * The BGZF blocks holding the BAM header are indepedent of alignment
286 BGZF blocks. Alignment records shorter than 64kB is guaranteed to be
287 fully contained in one BGZF block. This change is fully compatible
288 with the old version of samtools/picard.
290 Changes in other utilities:
292 * Updated export2sam.pl by Chris Saunders.
294 * Improved the sam2vcf.pl script.
296 * Added a Python version of varfilter.py by Aylwyn Scally.
298 (0.1.8: 11 July 2010, r613)
302 Beta Release 0.1.7 (10 November, 2009)
303 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
307 * Improved the indel caller in complex scenariors, in particular for
308 long reads. The indel caller is now able to make reasonable indel
309 calls from Craig Venter capillary reads.
311 * Rewrote single-end duplicate removal with improved
312 performance. Paired-end reads are not touched.
314 * Duplicate removal is now library aware. Samtools remove potential
315 PCR/optical dupliates inside a library rather than across libraries.
317 * SAM header is now fully parsed, although this functionality is not
318 used in merging and so on.
320 * In samtools merge, optionally take the input file name as RG-ID and
321 attach the RG tag to each alignment.
323 * Added FTP support in the RAZF library. RAZF-compressed reference
324 sequence can be retrieved remotely.
326 * Improved network support for Win32.
328 * Samtools sort and merge are now stable.
330 Changes in other utilities:
332 * Implemented sam2vcf.pl that converts the pileup format to the VCF
335 * This release of samtools is known to work with the latest
336 Bio-Samtools Perl module.
338 (0.1.7: 10 November 2009, r510)
342 Beta Release 0.1.6 (2 September, 2009)
343 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
347 * In tview, do not show a blank screen when no reads mapped to the
348 corresponding region.
350 * Implemented native HTTP support in the BGZF library. Samtools is now
351 able to directly open a BAM file on HTTP. HTTP proxy is also
352 supported via the "http_proxy" environmental variable.
354 * Samtools is now compitable with the MinGW (win32) compiler and the
357 * The calmd (or fillmd) command now calculates the NM tag and replaces
358 MD tags if they are wrong.
360 * The view command now recognizes and optionally prints FLAG in HEXs or
361 strings to make a SAM file more friendly to human eyes. This is a
362 samtools-C extension, not implemented in Picard for the time
363 being. Please type `samtools view -?' for more information.
365 * BAM files now have an end-of-file (EOF) marker to facilitate
366 truncation detection. A warning will be given if an on-disk BAM file
367 does not have this marker. The warning will be seen on BAM files
368 generated by an older version of samtools. It does NO harm.
370 * New key bindings in tview: `r' to show read names and `s' to show
371 reference skip (N operation) as deletions.
373 * Fixed a bug in `samtools merge -n'.
375 * Samtools merge now optionally copies the header of a user specified
376 SAM file to the resultant BAM output.
378 * Samtools pileup/tview works with a CIGAR with the first or the last
379 operation is an indel.
381 * Fixed a bug in bam_aux_get().
384 Changes in other utilies:
386 * Fixed wrong FLAG in maq2sam.
389 (0.1.6: 2 September 2009, r453)
393 Beta Release 0.1.5 (7 July, 2009)
394 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
398 * Support opening a BAM alignment on FTP. Users can now use "tview" to
399 view alignments at the NCBI ftp site. Please read manual for more
402 * In library, propagate errors rather than exit or complain assertion
405 * Simplified the building system and fixed compiling errors caused by
408 * Fixed an issue about lost header information when a SAM is imported
411 * Implemented "samtool.pl varFilter" which filters both SNPs and short
412 indels. This command replaces "indelFilter".
414 * Implemented "samtools.pl pileup2fq" to generate FASTQ consensus from
417 * In pileup, cap mapping quality at 60. This helps filtering when
418 different aligners are in use.
420 * In pileup, allow to output variant sites only.
422 * Made pileup generate correct calls in repetitive region. At the same
423 time, I am considering to implement a simplified model in SOAPsnp,
424 although this has not happened yet.
426 * In view, added '-u' option to output BAM without compression. This
427 option is preferred when the output is piped to other commands.
429 * In view, added '-l' and '-r' to get the alignments for one library or
430 read group. The "@RG" header lines are now partially parsed.
432 * Do not include command line utilities to libbam.a.
434 * Fixed memory leaks in pileup and bam_view1().
436 * Made faidx more tolerant to empty lines right before or after FASTA >
440 Changes in other utilities:
442 * Updated novo2sam.pl by Colin Hercus, the key developer of novoalign.
445 This release involves several modifications to the key code base which
446 may potentially introduce new bugs even though we have tried to minimize
447 this by testing on several examples. Please let us know if you catch
450 (0.1.5: 7 July 2009, r373)
454 Beta Release 0.1.4 (21 May, 2009)
455 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
459 * Added the 'rmdupse' command: removing duplicates for SE reads.
461 * Fixed a critical bug in the indel caller: clipped alignments are not
464 * Fixed a bug in the tview: gapped alignment may be incorrectly
467 * Unified the interface to BAM and SAM I/O. This is done by
468 implementing a wrapper on top of the old APIs and therefore old APIs
469 are still valid. The new I/O APIs also recognize the @SQ header
472 * Generate the MD tag.
474 * Generate "=" bases. However, the indel caller will not work when "="
477 * Enhanced support of color-read display (by Nils Homer).
479 * Implemented the GNU building system. However, currently the building
480 system does not generate libbam.a. We will improve this later. For
481 the time being, `make -f Makefile.generic' is preferred.
483 * Fixed a minor bug in pileup: the first read in a chromosome may be
486 * Fixed bugs in bam_aux.c. These bugs do not affect other components as
487 they were not used previously.
489 * Output the 'SM' tag from maq2sam.
491 (0.1.4: 21 May 2009, r297)
495 Beta Release 0.1.3 (15 April, 2009)
496 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
498 Notable changes in SAMtools:
500 * SAMtools is more consistent with the specification: a) '*' in the
501 QUAL field is allowed; b) the field separator is TAB only and SPACE
502 is treated as a character in a field; c) empty header is allowed.
504 * Implemented GLFv3 support in pileup.
506 * Fixed a severe bug in fixmate: strand information is wrongly
509 * Fixed a bug in alignment retrieval: alignments bridging n*16384bp are
510 not correctly retrieved sometimes.
512 * Fixed a bug in rmdup: segfault if unmapped reads are present.
514 * Move indel_filter.pl to samtools.pl and improved the filtering by
515 checking the actual number of alignments containing indels. The indel
516 pileup line is also changed a little to make this filtration easier.
518 * Fixed a minor bug in indexing: the bin number of an unmapped read is
521 * Added `flagstat' command to show statistics on the FLAG field.
523 * Improved indel caller by setting the maximum window size in local
526 Changes in other utilities:
528 * Fixed a bug in maq2sam: a tag name is obsolete.
530 * Improvement to wgsim: a) added support for SOLiD read simulation; b)
531 show the number of substitutions/indels/errors in read name; c)
532 considerable code clean up.
534 * Various converters: improved functionality in general.
536 * Updated the example SAM due to the previous bug in fixmate.
538 (0.1.3: 15 April 2009, r227)
542 Beta Release 0.1.2 (28 January, 2008)
543 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
545 Notable changes in SAMtools:
547 * Implemented a Bayesian indel caller. The new caller generate scores
548 and genotype and is potentially more accurate than Maq's indel
549 caller. The pileup format is also changed accordingly.
551 * Implemented rmdup command: remove potential PCR duplicates. Note that
552 this command ONLY works for FR orientation and requires ISIZE is
555 * Added fixmate command: fill in mate coordinates, ISIZE and mate
556 related flags from a name-sorted alignment.
558 * Fixed a bug in indexing: reads bridging 16x kbp were not retrieved.
560 * Allow to select reads shown in the pileup output with a mask.
562 * Generate GLFv2 from pileup.
564 * Added two more flags for flagging PCR/optical duplicates and for QC
567 * Fixed a bug in sort command: name sorting for large alignment did not
570 * Allow to completely disable RAZF (using Makefile.lite) as some people
571 have problem to compile it.
573 * Fixed a bug in import command when there are reads without
576 * Fixed a bug in tview: clipping broke the alignment viewer.
578 * Fixed a compiling error when _NO_CURSES is applied.
580 * Fixed a bug in merge command.
582 Changes in other utilities:
584 * Added wgsim, a paired-end reads simulator. Wgsim was adapted from
585 maq's reads simulator. Colin Hercus further improved it to allow
588 * Added wgsim_eval.pl, a script that evaluates the accuracy of
589 alignment on reads generated by wgsim.
591 * Added soap2sam.pl, a SOAP2->SAM converter. This converter does not
592 work properly when multiple hits are output.
594 * Added bowtie2sam.pl, a Bowtie->SAM converter. Only the top hit will
595 be retained when multiple hits are present.
597 * Fixed a bug in export2sam.pl for QC reads.
599 * Support RG tag at MAQ->SAM converter.
601 * Added novo2sam.pl, a NovoAlign->SAM converter. Multiple hits and
602 indel are not properly handled, though.
604 * Added zoom2sam.pl, a ZOOM->SAM converter. It only works with the
605 default Illumina output.
607 (0.1.2: 28 January 2008; r116)
611 Beta Release 0.1.1 (22 December, 2008)
612 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
614 The is the first public release of samtools. For more information,
615 please check the manual page `samtools.1' and the samtools website
616 http://samtools.sourceforge.net