1 Beta release 0.1.14 (16 March, 2011)
2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
4 This release implements a method for testing associations for case-control
5 data. The method does not call genotypes but instead sums over all genotype
6 configurations to compute a chi^2 based test statistics. It can be potentially
7 applied to comparing a pair of samples (e.g. a tumor-normal pair), but this
8 has not been evaluated on real data.
10 Another new feature is to make X chromosome variant calls when female and male
11 samples are both present. The user needs to provide a file indicating the
12 ploidy of each sample.
16 * Added `samtools mpileup -L' to skip INDEL calling in regions with
17 excessively high coverage. Such regions dramatically slow down mpileup.
19 * Added `bcftools view -F' to parse BCF files generated by samtools r921 or
20 older which encode PL in a different way.
22 (0.1.14: 16 March 2011, r930:163)
26 Beta release 0.1.13 (1 March, 2011)
27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
29 The most important though largely invisible modification is the change of the
30 order of genotypes in the PL VCF/BCF tag. This is to conform the upcoming VCF
31 spec v4.1. The change means that 0.1.13 is not backward compatible with VCF/BCF
32 generated by samtools older than r921 inclusive. VCF/BCF generated by the new
33 samtools will contain a line `##fileformat=VCFv4.1' as well as the samtools
36 Single Individual Haplotyping (SIH) is added as an experimental feature. It
37 originally aims to produce haploid consensus from fosmid pool sequencing, but
38 also works with short-read data. For short reads, phased blocks are usually too
39 short to be useful in many applications, but they can help to rule out part of
40 SNPs close to INDELs or between copies of CNVs.
43 Other notable changes in samtools:
45 * Construct per-sample consensus to reduce the effect of nearby SNPs in INDEL
46 calling. This reduces the power but improves specificity.
48 * Improved sorting order checking in indexing. Now indexing is the preferred way
49 to check if a BAM is sorted.
51 * Added a switch `-E' to mpileup and calmd. This option uses an alternative way
52 to apply BAQ, which increases sensistivity, especially to MNPs, at the cost of
53 a little loss in specificity.
55 * Added `mpileup -A' to allow to use reads in anomalous pairs in SNP calling.
57 * Added `mpileup -m' to allow fine control of the collection of INDEL candidates.
59 * Added `mpileup -S' to compute per-sample strand bias P-value.
61 * Added `mpileup -G' to exclude read groups in variant calling.
63 * Fixed segfault in indel calling related to unmapped and refskip reads.
65 * Fixed an integer overflow in INDEL calling. This bug produces wrong INDEL
66 genotypes for longer short INDELs, typically over 10bp.
68 * Fixed a bug in tview on big-endian machines.
70 * Fixed a very rare memory issue in bam_md.c
72 * Fixed an out-of-boundary bug in mpileup when the read base is `N'.
74 * Fixed a compiling error when the knetfile library is not used. Fixed a
75 library compiling error due to the lack of bam_nt16_nt4_table[] table.
76 Suppress a compiling warning related to the latest zlib.
79 Other notable changes in bcftools:
81 * Updated the BCF spec.
83 * Added the `FQ' VCF INFO field, which gives the phred-scaled probability
84 of all samples being the same (identical to the reference or all homozygous
85 variants). Option `view -f' has been dropped.
87 * Implementated of "vcfutils.pl vcf2fq" to generate a consensus sequence
88 similar to "samtools.pl pileup2fq".
90 * Make sure the GT FORMAT field is always the first FORMAT to conform the VCF
91 spec. Drop bcf-fix.pl.
93 * Output bcftools specific INFO and FORMAT in the VCF header.
95 * Added `view -s' to call variants from a subset of samples.
97 * Properly convert VCF to BCF with a user provided sequence dictionary. Nonetheless,
98 custom fields are still unparsed and will be stored as a missing value.
100 * Fixed a minor bug in Fisher's exact test; the results are rarely changed.
103 (0.1.13: 1 March 2011, r926:134)
107 Beta release 0.1.12a (2 December, 2010)
108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
110 This is another bug fix release:
112 * Fixed a memory violation in mpileup, which causes segfault. Release
113 0.1.9 and above are affected.
115 * Fixed a memory violation in the indel caller, which does not causes
116 segfault, but may potentially affect deletion calls in an unexpected
117 way. Release 0.1.10 and above are affected.
119 * Fixed a bug in computing r-square in bcftools. Few are using this
120 functionality and it only has minor effect.
122 * Fixed a memory leak in bam_fetch().
124 * Fixed a bug in writing meta information to the BAM index for the last
125 sequence. This bug is invisible to most users, but it is a bug anyway.
127 * Fixed a bug in bcftools which causes false "DP4=0,0,0,0" annotations.
129 (0.1.12: 2 December 2010, r862)
133 Beta release 0.1.11 (21 November, 2010)
134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
136 This is mainly a bug fix release:
138 * Fixed a bug in random retrieval (since 0.1.8). It occurs when reads
139 are retrieved from a small region containing no reads.
141 * Fixed a bug in pileup (since 0.1.9). The bug causes an assertion
142 failure when the first CIGAR operation is a deletion.
144 * Improved fault tolerence in remote access.
146 One minor feature has been implemented in bcftools:
148 * Added a reference-free variant calling mode. In this mode, a site is
149 regarded as a variat iff the sample(s) contains two or more alleles;
150 the meaning of the QUAL field in the VCF output is changed
151 accordingly. Effectively, the reference allele is irrelevant to the
152 result in the new mode, although the reference sequence has to be
153 used in realignment when SAMtools computes genotype likelihoods.
155 In addition, since 0.1.10, the `pileup' command has been deprecated by
156 `mpileup' which is more powerful and more accurate. The `pileup' command
157 will not be removed in the next few releases, but new features will not
160 (0.1.11: 21 November 2010, r851)
164 Beta Release 0.1.10 (16 November, 2010)
165 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
167 This release is featured as the first major improvement to the indel
168 caller. The method is similar to the old one implemented in the pileup
169 command, but the details are handled more carefully both in theory and
170 in practice. As a result, the new indel caller usually gives more
171 accurate indel calls, though at the cost of sensitivity. The caller is
172 implemented in the mpileup command and is invoked by default. It works
173 with multiple samples.
175 Other notable changes:
177 * With the -r option, the calmd command writes the difference between
178 the original base quality and the BAQ capped base quality at the BQ
179 tag but does not modify the base quality. Please use -Ar to overwrite
180 the original base quality (the 0.1.9 behavior).
182 * Allow to set a maximum per-sample read depth to reduce memory. In
183 0.1.9, most of memory is wasted for the ultra high read depth in some
184 regions (e.g. the chr1 centromere).
186 * Optionally write per-sample read depth and per-sample strand bias
189 * Compute equal-tail (Bayesian) credible interval of site allele
190 frequency at the CI95 VCF annotation.
192 * Merged the vcfutils.pl varFilter and filter4vcf for better SNP/indel
195 (0.1.10: 16 November 2010, r829)
199 Beta Release 0.1.9 (27 October, 2010)
200 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
202 This release is featured as the first major improvement to the samtools'
203 SNP caller. It comes with a revised MAQ error model, the support of
204 multi-sample SNP calling and the computation of base alignment quality
207 The revised MAQ error model is based on the original model. It solves an
208 issue of miscalling SNPs in repetitive regions. Althought such SNPs can
209 usually be filtered at a later step, they mess up unfiltered calls. This
210 is a theoretical flaw in the original model. The revised MAQ model
211 deprecates the orginal MAQ model and the simplified SOAPsnp model.
213 Multi-sample SNP calling is separated in two steps. The first is done by
214 samtools mpileup and the second by a new program, bcftools, which is
215 included in the samtools source code tree. Multi-sample SNP calling also
216 works for single sample and has the advantage of enabling more powerful
217 filtration. It is likely to deprecate pileup in future once a proper
218 indel calling method is implemented.
220 BAQ is the Phred-scaled probability of a read base being wrongly
221 aligned. Capping base quality by BAQ has been shown to be very effective
222 in suppressing false SNPs caused by misalignments around indels or in
223 low-complexity regions with acceptable compromise on computation
224 time. This strategy is highly recommended and can be used with other SNP
227 In addition to the three major improvements, other notable changes are:
229 * Changes to the pileup format. A reference skip (the N CIGAR operator)
230 is shown as '<' or '>' depending on the strand. Tview is also changed
233 * Accelerated pileup. The plain pileup is about 50% faster.
235 * Regional merge. The merge command now accepts a new option to merge
236 files in a specified region.
238 * Fixed a bug in bgzip and razip which causes source files to be
239 deleted even if option -c is applied.
241 * In APIs, propogate errors to downstream callers and make samtools
242 return non-zero values once errors occur.
244 (0.1.9: 27 October 2010, r783)
248 Beta Release 0.1.8 (11 July, 2010)
249 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
251 Notable functional changes:
253 * Added the `reheader' command which replaces a BAM header with a new
254 header. This command is much faster than replacing header by
255 BAM->SAM->BAM conversions.
257 * Added the `mpileup' command which computes the pileup of multiple
260 * The `index' command now stores the number of mapped and unmapped
261 reads in the index file. This information can be retrieved quickly by
262 the new `idxstats' command.
264 * By default, pileup used the SOAPsnp model for SNP calling. This
265 avoids the floating overflow in the MAQ model which leads to spurious
266 calls in repetitive regions, although these calls will be immediately
267 filtered by varFilter.
269 * The `tview' command now correctly handles CIGARs like 7I10M and
270 10M1P1I10M which cause assertion failure in earlier versions.
272 * Tview accepts a region like `=10,000' where `=' stands for the
273 current sequence name. This saves typing for long sequence names.
275 * Added the `-d' option to `pileup' which avoids slow indel calling
276 in ultradeep regions by subsampling reads locally.
278 * Added the `-R' option to `view' which retrieves alignments in read
279 groups listed in the specified file.
281 Performance improvements:
283 * The BAM->SAM conversion is up to twice faster, depending on the
284 characteristic of the input.
286 * Parsing SAM headers with a lot of reference sequences is now much
289 * The number of lseek() calls per query is reduced when the query
290 region contains no read alignments.
294 * Fixed an issue in the indel caller that leads to miscall of indels.
295 Note that this solution may not work well when the sequencing indel
296 error rate is higher than the rate of SNPs.
298 * Fixed another issue in the indel caller which may lead to incorrect
301 * Fixed a bug in `sort' when option `-o' is applied.
303 * Fixed a bug in `view -r'.
305 APIs and other changes:
307 * Added iterator interfaces to random access and pileup. The callback
308 interfaces directly call the iterator interfaces.
310 * The BGZF blocks holding the BAM header are indepedent of alignment
311 BGZF blocks. Alignment records shorter than 64kB is guaranteed to be
312 fully contained in one BGZF block. This change is fully compatible
313 with the old version of samtools/picard.
315 Changes in other utilities:
317 * Updated export2sam.pl by Chris Saunders.
319 * Improved the sam2vcf.pl script.
321 * Added a Python version of varfilter.py by Aylwyn Scally.
323 (0.1.8: 11 July 2010, r613)
327 Beta Release 0.1.7 (10 November, 2009)
328 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
332 * Improved the indel caller in complex scenariors, in particular for
333 long reads. The indel caller is now able to make reasonable indel
334 calls from Craig Venter capillary reads.
336 * Rewrote single-end duplicate removal with improved
337 performance. Paired-end reads are not touched.
339 * Duplicate removal is now library aware. Samtools remove potential
340 PCR/optical dupliates inside a library rather than across libraries.
342 * SAM header is now fully parsed, although this functionality is not
343 used in merging and so on.
345 * In samtools merge, optionally take the input file name as RG-ID and
346 attach the RG tag to each alignment.
348 * Added FTP support in the RAZF library. RAZF-compressed reference
349 sequence can be retrieved remotely.
351 * Improved network support for Win32.
353 * Samtools sort and merge are now stable.
355 Changes in other utilities:
357 * Implemented sam2vcf.pl that converts the pileup format to the VCF
360 * This release of samtools is known to work with the latest
361 Bio-Samtools Perl module.
363 (0.1.7: 10 November 2009, r510)
367 Beta Release 0.1.6 (2 September, 2009)
368 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
372 * In tview, do not show a blank screen when no reads mapped to the
373 corresponding region.
375 * Implemented native HTTP support in the BGZF library. Samtools is now
376 able to directly open a BAM file on HTTP. HTTP proxy is also
377 supported via the "http_proxy" environmental variable.
379 * Samtools is now compitable with the MinGW (win32) compiler and the
382 * The calmd (or fillmd) command now calculates the NM tag and replaces
383 MD tags if they are wrong.
385 * The view command now recognizes and optionally prints FLAG in HEXs or
386 strings to make a SAM file more friendly to human eyes. This is a
387 samtools-C extension, not implemented in Picard for the time
388 being. Please type `samtools view -?' for more information.
390 * BAM files now have an end-of-file (EOF) marker to facilitate
391 truncation detection. A warning will be given if an on-disk BAM file
392 does not have this marker. The warning will be seen on BAM files
393 generated by an older version of samtools. It does NO harm.
395 * New key bindings in tview: `r' to show read names and `s' to show
396 reference skip (N operation) as deletions.
398 * Fixed a bug in `samtools merge -n'.
400 * Samtools merge now optionally copies the header of a user specified
401 SAM file to the resultant BAM output.
403 * Samtools pileup/tview works with a CIGAR with the first or the last
404 operation is an indel.
406 * Fixed a bug in bam_aux_get().
409 Changes in other utilies:
411 * Fixed wrong FLAG in maq2sam.
414 (0.1.6: 2 September 2009, r453)
418 Beta Release 0.1.5 (7 July, 2009)
419 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
423 * Support opening a BAM alignment on FTP. Users can now use "tview" to
424 view alignments at the NCBI ftp site. Please read manual for more
427 * In library, propagate errors rather than exit or complain assertion
430 * Simplified the building system and fixed compiling errors caused by
433 * Fixed an issue about lost header information when a SAM is imported
436 * Implemented "samtool.pl varFilter" which filters both SNPs and short
437 indels. This command replaces "indelFilter".
439 * Implemented "samtools.pl pileup2fq" to generate FASTQ consensus from
442 * In pileup, cap mapping quality at 60. This helps filtering when
443 different aligners are in use.
445 * In pileup, allow to output variant sites only.
447 * Made pileup generate correct calls in repetitive region. At the same
448 time, I am considering to implement a simplified model in SOAPsnp,
449 although this has not happened yet.
451 * In view, added '-u' option to output BAM without compression. This
452 option is preferred when the output is piped to other commands.
454 * In view, added '-l' and '-r' to get the alignments for one library or
455 read group. The "@RG" header lines are now partially parsed.
457 * Do not include command line utilities to libbam.a.
459 * Fixed memory leaks in pileup and bam_view1().
461 * Made faidx more tolerant to empty lines right before or after FASTA >
465 Changes in other utilities:
467 * Updated novo2sam.pl by Colin Hercus, the key developer of novoalign.
470 This release involves several modifications to the key code base which
471 may potentially introduce new bugs even though we have tried to minimize
472 this by testing on several examples. Please let us know if you catch
475 (0.1.5: 7 July 2009, r373)
479 Beta Release 0.1.4 (21 May, 2009)
480 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
484 * Added the 'rmdupse' command: removing duplicates for SE reads.
486 * Fixed a critical bug in the indel caller: clipped alignments are not
489 * Fixed a bug in the tview: gapped alignment may be incorrectly
492 * Unified the interface to BAM and SAM I/O. This is done by
493 implementing a wrapper on top of the old APIs and therefore old APIs
494 are still valid. The new I/O APIs also recognize the @SQ header
497 * Generate the MD tag.
499 * Generate "=" bases. However, the indel caller will not work when "="
502 * Enhanced support of color-read display (by Nils Homer).
504 * Implemented the GNU building system. However, currently the building
505 system does not generate libbam.a. We will improve this later. For
506 the time being, `make -f Makefile.generic' is preferred.
508 * Fixed a minor bug in pileup: the first read in a chromosome may be
511 * Fixed bugs in bam_aux.c. These bugs do not affect other components as
512 they were not used previously.
514 * Output the 'SM' tag from maq2sam.
516 (0.1.4: 21 May 2009, r297)
520 Beta Release 0.1.3 (15 April, 2009)
521 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
523 Notable changes in SAMtools:
525 * SAMtools is more consistent with the specification: a) '*' in the
526 QUAL field is allowed; b) the field separator is TAB only and SPACE
527 is treated as a character in a field; c) empty header is allowed.
529 * Implemented GLFv3 support in pileup.
531 * Fixed a severe bug in fixmate: strand information is wrongly
534 * Fixed a bug in alignment retrieval: alignments bridging n*16384bp are
535 not correctly retrieved sometimes.
537 * Fixed a bug in rmdup: segfault if unmapped reads are present.
539 * Move indel_filter.pl to samtools.pl and improved the filtering by
540 checking the actual number of alignments containing indels. The indel
541 pileup line is also changed a little to make this filtration easier.
543 * Fixed a minor bug in indexing: the bin number of an unmapped read is
546 * Added `flagstat' command to show statistics on the FLAG field.
548 * Improved indel caller by setting the maximum window size in local
551 Changes in other utilities:
553 * Fixed a bug in maq2sam: a tag name is obsolete.
555 * Improvement to wgsim: a) added support for SOLiD read simulation; b)
556 show the number of substitutions/indels/errors in read name; c)
557 considerable code clean up.
559 * Various converters: improved functionality in general.
561 * Updated the example SAM due to the previous bug in fixmate.
563 (0.1.3: 15 April 2009, r227)
567 Beta Release 0.1.2 (28 January, 2008)
568 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
570 Notable changes in SAMtools:
572 * Implemented a Bayesian indel caller. The new caller generate scores
573 and genotype and is potentially more accurate than Maq's indel
574 caller. The pileup format is also changed accordingly.
576 * Implemented rmdup command: remove potential PCR duplicates. Note that
577 this command ONLY works for FR orientation and requires ISIZE is
580 * Added fixmate command: fill in mate coordinates, ISIZE and mate
581 related flags from a name-sorted alignment.
583 * Fixed a bug in indexing: reads bridging 16x kbp were not retrieved.
585 * Allow to select reads shown in the pileup output with a mask.
587 * Generate GLFv2 from pileup.
589 * Added two more flags for flagging PCR/optical duplicates and for QC
592 * Fixed a bug in sort command: name sorting for large alignment did not
595 * Allow to completely disable RAZF (using Makefile.lite) as some people
596 have problem to compile it.
598 * Fixed a bug in import command when there are reads without
601 * Fixed a bug in tview: clipping broke the alignment viewer.
603 * Fixed a compiling error when _NO_CURSES is applied.
605 * Fixed a bug in merge command.
607 Changes in other utilities:
609 * Added wgsim, a paired-end reads simulator. Wgsim was adapted from
610 maq's reads simulator. Colin Hercus further improved it to allow
613 * Added wgsim_eval.pl, a script that evaluates the accuracy of
614 alignment on reads generated by wgsim.
616 * Added soap2sam.pl, a SOAP2->SAM converter. This converter does not
617 work properly when multiple hits are output.
619 * Added bowtie2sam.pl, a Bowtie->SAM converter. Only the top hit will
620 be retained when multiple hits are present.
622 * Fixed a bug in export2sam.pl for QC reads.
624 * Support RG tag at MAQ->SAM converter.
626 * Added novo2sam.pl, a NovoAlign->SAM converter. Multiple hits and
627 indel are not properly handled, though.
629 * Added zoom2sam.pl, a ZOOM->SAM converter. It only works with the
630 default Illumina output.
632 (0.1.2: 28 January 2008; r116)
636 Beta Release 0.1.1 (22 December, 2008)
637 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
639 The is the first public release of samtools. For more information,
640 please check the manual page `samtools.1' and the samtools website
641 http://samtools.sourceforge.net