1 Beta Release 0.1.19 (15 March, 2013)
2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
4 Notable changes in samtools and bcftools:
6 * The latest source code and development moved to github,
7 http://github.com/samtools/samtools
9 * Many important bugfixes and contributions by many people. Thanks to all!
11 * Performance improvements (multi-threading)
13 * Important changes in calling, see
17 * New annotations useful for filtering (RPB, HWE, QBD, MDV)
19 * New tools, bamcheck and plot-bamcheck
21 * New features in samtools tview
25 For a detailed list of commits, please see
26 http://github.com/samtools/samtools/commits/master
28 (0.1.19: 15 March 2013, commit 96b5f2294ac0054230e88913c4983d548069ea4e)
31 Beta Release 0.1.18 (2 September, 2011)
32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
34 Notable changes in samtools:
36 * Support the new =/X CIGAR operators (by Peter Cock).
38 * Allow to subsample BAM while keeping the pairing intact (view -s).
40 * Implemented variant distance bias as a new filter (by Petr Danecek).
42 * Bugfix: huge memory usage during indexing
44 * Bugfix: use of uninitialized variable in mpileup (rare)
46 * Bugfix: wrong BAQ probability (rare)
48 Notable changes in bcftools:
50 * Support indel in the contrast caller.
52 * Bugfix: LRT2=nan in rare cases
54 (0.1.18: 2 September 2011, r982:295)
58 Beta Release 0.1.17 (6 July, 2011)
59 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
61 With the maturity of `mpileup' and the lack of update in the `pileup' command,
62 the `pileup' command is now formally dropped. Most of the pileup functionality,
63 such as outputting mapping quality and read positions, have been added
66 Since this release, `bcftools view' is able to perform contrast SNP calling
67 (option -T) for discovering de novo and/or somatic mutations between a pair of
68 samples or in a family trio. Potential mutations are scored by a log likelihood
69 ratio, which is very simple in math, but should be comparable to more
70 sophisticated methods. Note that getting the score is only the very first step.
71 A lot more need to be done to reduce systematical errors due to mapping and
72 reference errors and structural variations.
74 Other notable changes in samtools:
76 * Improved sorting order checking during indexing.
78 * Improved region parsing. Colons in reference sequence names are parsed
81 * Fixed an issue where mpileup does not apply BAQ for the first few reads when
82 a region is specified.
84 * Fixed an issue where `faidx' does not work with FASTA files with long lines.
86 * Bugfix: wrong SP genotype information in the BCF output.
88 Other notable changes in bcftools:
90 * Output the ML esitmate of the allele count.
92 * Added the HWE plus F<0 filter to varFilter. For multiple samples, it
93 effectively filters false heterozygous calls around centromeres.
95 * For association mapping, perform both 1-degree and 2-degree test. The
96 2-degree test is conservative but more robust to HWE violation.
98 (0.1.17: 6 July 2011, r973:277)
102 Beta Release 0.1.16 (21 April, 2011)
103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
105 Notable changes in samtools:
107 * Support the new SAM/BAM type `B' in the latest SAM spec v1.4.
109 * When the output file of `samtools merge' exists, do not overwrite it unless
110 a new command-line option `-f' is applied.
112 * Bugfix: BED support is not working when the input BED is not sorted.
114 * Bugfix: some reads without coordinates but given on the reverse strand are
117 Notable changes in bcftools:
119 * Code cleanup: separated max-likelihood inference and Bayesian inference.
121 * Test Hardy-Weinberg equilibrium with a likelihood-ratio test.
123 * Provided another association test P-value by likelihood-ratio test.
125 * Use Brent's method to estimate the site allele frequency when EM converges
126 slowly. The resulting ML estimate of allele frequnecy is more accurate.
128 * Added the `ldpair' command, which computes r^2 between SNP pairs given in
131 Also, the `pileup' command, which has been deprecated by `mpileup' since
132 version 0.1.10, will be dropped in the next release. The old `pileup' command
133 is substandard and causing a lot of confusion.
135 (0.1.16: 21 April 2011, r963:234)
139 Beta Release 0.1.15 (10 April, 2011)
140 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
144 * Allow to perform variant calling or to extract information in multiple
145 regions specified by a BED file (`samtools mpileup -l', `samtools view -L'
146 and `bcftools view -l').
148 * Added the `depth' command to samtools to compute the per-base depth with a
149 simpler interface. File `bam2depth.c', which implements this command, is the
150 recommended example on how to use the mpileup APIs.
152 * Estimate genotype frequencies with ML; perform chi^2 based Hardy-Weinberg
153 test using this estimate.
155 * For `samtools view', when `-R' is specified, drop read groups in the header
156 that are not contained in the specified file.
158 * For `samtools flagstat', separate QC-pass and QC-fail reads.
160 * Improved the command line help of `samtools mpileup' and `bcftools view'.
162 * Use a global variable to control the verbose level of samtools stderr
163 output. Nonetheless, it has not been full utilized.
165 * Fixed an issue in association test which may report false associations,
166 possibly due to floating point underflow.
168 (0.1.15: 10 April 2011, r949:203)
172 Beta release 0.1.14 (21 March, 2011)
173 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
175 This release implements a method for testing associations for case-control
176 data. The method does not call genotypes but instead sums over all genotype
177 configurations to compute a chi^2 based test statistics. It can be potentially
178 applied to comparing a pair of samples (e.g. a tumor-normal pair), but this
179 has not been evaluated on real data.
181 Another new feature is to make X chromosome variant calls when female and male
182 samples are both present. The user needs to provide a file indicating the
183 ploidy of each sample (see also manual bcftools/bcftools.1).
185 Other notable changes:
187 * Added `bcftools view -F' to parse BCF files generated by samtools r921 or
188 older which encodes PL in a different way.
190 * Changed the behavior of `bcftools view -s'. Now when a list of samples is
191 provided, the samples in the output will be reordered to match the ordering
192 in the sample list. This change is mainly designed for association test.
194 * Sped up `bcftools view -v' for target sequencing given thousands of samples.
195 Also added a new option `view -d' to skip loci where only a few samples are
198 * Dropped HWE test. This feature has never been implemented properly. An EM
199 should be much better. To be implemented in future.
201 * Added the `cat' command to samtools. This command concatenate BAMs with
202 identical sequence dictionaries in an efficient way. Modified from bam_cat.c
203 written by Chris Saunders.
205 * Added `samtools view -1' to write BAMs at a low compression level but twice
206 faster to create. The `sort' command generates temporary files at a low
207 compression level as well.
209 * Added `samtools mpileup -6' to accept "BAM" with Illumina 1.3+ quality
210 strings (strictly speaking, such a file is not BAM).
212 * Added `samtools mpileup -L' to skip INDEL calling in regions with
213 excessively high coverage. Such regions dramatically slow down mpileup.
215 * Updated `misc/export2sam.pl', provided by Chris Saunders from Illumina Inc.
217 (0.1.14: 21 March 2011, r933:170)
221 Beta release 0.1.13 (1 March, 2011)
222 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 The most important though largely invisible modification is the change of the
225 order of genotypes in the PL VCF/BCF tag. This is to conform the upcoming VCF
226 spec v4.1. The change means that 0.1.13 is not backward compatible with VCF/BCF
227 generated by samtools older than r921 inclusive. VCF/BCF generated by the new
228 samtools will contain a line `##fileformat=VCFv4.1' as well as the samtools
231 Single Individual Haplotyping (SIH) is added as an experimental feature. It
232 originally aims to produce haploid consensus from fosmid pool sequencing, but
233 also works with short-read data. For short reads, phased blocks are usually too
234 short to be useful in many applications, but they can help to rule out part of
235 SNPs close to INDELs or between copies of CNVs.
238 Other notable changes in samtools:
240 * Construct per-sample consensus to reduce the effect of nearby SNPs in INDEL
241 calling. This reduces the power but improves specificity.
243 * Improved sorting order checking in indexing. Now indexing is the preferred way
244 to check if a BAM is sorted.
246 * Added a switch `-E' to mpileup and calmd. This option uses an alternative way
247 to apply BAQ, which increases sensistivity, especially to MNPs, at the cost of
248 a little loss in specificity.
250 * Added `mpileup -A' to allow to use reads in anomalous pairs in SNP calling.
252 * Added `mpileup -m' to allow fine control of the collection of INDEL candidates.
254 * Added `mpileup -S' to compute per-sample strand bias P-value.
256 * Added `mpileup -G' to exclude read groups in variant calling.
258 * Fixed segfault in indel calling related to unmapped and refskip reads.
260 * Fixed an integer overflow in INDEL calling. This bug produces wrong INDEL
261 genotypes for longer short INDELs, typically over 10bp.
263 * Fixed a bug in tview on big-endian machines.
265 * Fixed a very rare memory issue in bam_md.c
267 * Fixed an out-of-boundary bug in mpileup when the read base is `N'.
269 * Fixed a compiling error when the knetfile library is not used. Fixed a
270 library compiling error due to the lack of bam_nt16_nt4_table[] table.
271 Suppress a compiling warning related to the latest zlib.
274 Other notable changes in bcftools:
276 * Updated the BCF spec.
278 * Added the `FQ' VCF INFO field, which gives the phred-scaled probability
279 of all samples being the same (identical to the reference or all homozygous
280 variants). Option `view -f' has been dropped.
282 * Implementated of "vcfutils.pl vcf2fq" to generate a consensus sequence
283 similar to "samtools.pl pileup2fq".
285 * Make sure the GT FORMAT field is always the first FORMAT to conform the VCF
286 spec. Drop bcf-fix.pl.
288 * Output bcftools specific INFO and FORMAT in the VCF header.
290 * Added `view -s' to call variants from a subset of samples.
292 * Properly convert VCF to BCF with a user provided sequence dictionary. Nonetheless,
293 custom fields are still unparsed and will be stored as a missing value.
295 * Fixed a minor bug in Fisher's exact test; the results are rarely changed.
298 (0.1.13: 1 March 2011, r926:134)
302 Beta release 0.1.12a (2 December, 2010)
303 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
305 This is another bug fix release:
307 * Fixed a memory violation in mpileup, which causes segfault. Release
308 0.1.9 and above are affected.
310 * Fixed a memory violation in the indel caller, which does not causes
311 segfault, but may potentially affect deletion calls in an unexpected
312 way. Release 0.1.10 and above are affected.
314 * Fixed a bug in computing r-square in bcftools. Few are using this
315 functionality and it only has minor effect.
317 * Fixed a memory leak in bam_fetch().
319 * Fixed a bug in writing meta information to the BAM index for the last
320 sequence. This bug is invisible to most users, but it is a bug anyway.
322 * Fixed a bug in bcftools which causes false "DP4=0,0,0,0" annotations.
324 (0.1.12: 2 December 2010, r862)
328 Beta release 0.1.11 (21 November, 2010)
329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
331 This is mainly a bug fix release:
333 * Fixed a bug in random retrieval (since 0.1.8). It occurs when reads
334 are retrieved from a small region containing no reads.
336 * Fixed a bug in pileup (since 0.1.9). The bug causes an assertion
337 failure when the first CIGAR operation is a deletion.
339 * Improved fault tolerence in remote access.
341 One minor feature has been implemented in bcftools:
343 * Added a reference-free variant calling mode. In this mode, a site is
344 regarded as a variat iff the sample(s) contains two or more alleles;
345 the meaning of the QUAL field in the VCF output is changed
346 accordingly. Effectively, the reference allele is irrelevant to the
347 result in the new mode, although the reference sequence has to be
348 used in realignment when SAMtools computes genotype likelihoods.
350 In addition, since 0.1.10, the `pileup' command has been deprecated by
351 `mpileup' which is more powerful and more accurate. The `pileup' command
352 will not be removed in the next few releases, but new features will not
355 (0.1.11: 21 November 2010, r851)
359 Beta Release 0.1.10 (16 November, 2010)
360 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
362 This release is featured as the first major improvement to the indel
363 caller. The method is similar to the old one implemented in the pileup
364 command, but the details are handled more carefully both in theory and
365 in practice. As a result, the new indel caller usually gives more
366 accurate indel calls, though at the cost of sensitivity. The caller is
367 implemented in the mpileup command and is invoked by default. It works
368 with multiple samples.
370 Other notable changes:
372 * With the -r option, the calmd command writes the difference between
373 the original base quality and the BAQ capped base quality at the BQ
374 tag but does not modify the base quality. Please use -Ar to overwrite
375 the original base quality (the 0.1.9 behavior).
377 * Allow to set a maximum per-sample read depth to reduce memory. In
378 0.1.9, most of memory is wasted for the ultra high read depth in some
379 regions (e.g. the chr1 centromere).
381 * Optionally write per-sample read depth and per-sample strand bias
384 * Compute equal-tail (Bayesian) credible interval of site allele
385 frequency at the CI95 VCF annotation.
387 * Merged the vcfutils.pl varFilter and filter4vcf for better SNP/indel
390 (0.1.10: 16 November 2010, r829)
394 Beta Release 0.1.9 (27 October, 2010)
395 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
397 This release is featured as the first major improvement to the samtools'
398 SNP caller. It comes with a revised MAQ error model, the support of
399 multi-sample SNP calling and the computation of base alignment quality
402 The revised MAQ error model is based on the original model. It solves an
403 issue of miscalling SNPs in repetitive regions. Althought such SNPs can
404 usually be filtered at a later step, they mess up unfiltered calls. This
405 is a theoretical flaw in the original model. The revised MAQ model
406 deprecates the orginal MAQ model and the simplified SOAPsnp model.
408 Multi-sample SNP calling is separated in two steps. The first is done by
409 samtools mpileup and the second by a new program, bcftools, which is
410 included in the samtools source code tree. Multi-sample SNP calling also
411 works for single sample and has the advantage of enabling more powerful
412 filtration. It is likely to deprecate pileup in future once a proper
413 indel calling method is implemented.
415 BAQ is the Phred-scaled probability of a read base being wrongly
416 aligned. Capping base quality by BAQ has been shown to be very effective
417 in suppressing false SNPs caused by misalignments around indels or in
418 low-complexity regions with acceptable compromise on computation
419 time. This strategy is highly recommended and can be used with other SNP
422 In addition to the three major improvements, other notable changes are:
424 * Changes to the pileup format. A reference skip (the N CIGAR operator)
425 is shown as '<' or '>' depending on the strand. Tview is also changed
428 * Accelerated pileup. The plain pileup is about 50% faster.
430 * Regional merge. The merge command now accepts a new option to merge
431 files in a specified region.
433 * Fixed a bug in bgzip and razip which causes source files to be
434 deleted even if option -c is applied.
436 * In APIs, propogate errors to downstream callers and make samtools
437 return non-zero values once errors occur.
439 (0.1.9: 27 October 2010, r783)
443 Beta Release 0.1.8 (11 July, 2010)
444 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
446 Notable functional changes:
448 * Added the `reheader' command which replaces a BAM header with a new
449 header. This command is much faster than replacing header by
450 BAM->SAM->BAM conversions.
452 * Added the `mpileup' command which computes the pileup of multiple
455 * The `index' command now stores the number of mapped and unmapped
456 reads in the index file. This information can be retrieved quickly by
457 the new `idxstats' command.
459 * By default, pileup used the SOAPsnp model for SNP calling. This
460 avoids the floating overflow in the MAQ model which leads to spurious
461 calls in repetitive regions, although these calls will be immediately
462 filtered by varFilter.
464 * The `tview' command now correctly handles CIGARs like 7I10M and
465 10M1P1I10M which cause assertion failure in earlier versions.
467 * Tview accepts a region like `=10,000' where `=' stands for the
468 current sequence name. This saves typing for long sequence names.
470 * Added the `-d' option to `pileup' which avoids slow indel calling
471 in ultradeep regions by subsampling reads locally.
473 * Added the `-R' option to `view' which retrieves alignments in read
474 groups listed in the specified file.
476 Performance improvements:
478 * The BAM->SAM conversion is up to twice faster, depending on the
479 characteristic of the input.
481 * Parsing SAM headers with a lot of reference sequences is now much
484 * The number of lseek() calls per query is reduced when the query
485 region contains no read alignments.
489 * Fixed an issue in the indel caller that leads to miscall of indels.
490 Note that this solution may not work well when the sequencing indel
491 error rate is higher than the rate of SNPs.
493 * Fixed another issue in the indel caller which may lead to incorrect
496 * Fixed a bug in `sort' when option `-o' is applied.
498 * Fixed a bug in `view -r'.
500 APIs and other changes:
502 * Added iterator interfaces to random access and pileup. The callback
503 interfaces directly call the iterator interfaces.
505 * The BGZF blocks holding the BAM header are indepedent of alignment
506 BGZF blocks. Alignment records shorter than 64kB is guaranteed to be
507 fully contained in one BGZF block. This change is fully compatible
508 with the old version of samtools/picard.
510 Changes in other utilities:
512 * Updated export2sam.pl by Chris Saunders.
514 * Improved the sam2vcf.pl script.
516 * Added a Python version of varfilter.py by Aylwyn Scally.
518 (0.1.8: 11 July 2010, r613)
522 Beta Release 0.1.7 (10 November, 2009)
523 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
527 * Improved the indel caller in complex scenariors, in particular for
528 long reads. The indel caller is now able to make reasonable indel
529 calls from Craig Venter capillary reads.
531 * Rewrote single-end duplicate removal with improved
532 performance. Paired-end reads are not touched.
534 * Duplicate removal is now library aware. Samtools remove potential
535 PCR/optical dupliates inside a library rather than across libraries.
537 * SAM header is now fully parsed, although this functionality is not
538 used in merging and so on.
540 * In samtools merge, optionally take the input file name as RG-ID and
541 attach the RG tag to each alignment.
543 * Added FTP support in the RAZF library. RAZF-compressed reference
544 sequence can be retrieved remotely.
546 * Improved network support for Win32.
548 * Samtools sort and merge are now stable.
550 Changes in other utilities:
552 * Implemented sam2vcf.pl that converts the pileup format to the VCF
555 * This release of samtools is known to work with the latest
556 Bio-Samtools Perl module.
558 (0.1.7: 10 November 2009, r510)
562 Beta Release 0.1.6 (2 September, 2009)
563 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
567 * In tview, do not show a blank screen when no reads mapped to the
568 corresponding region.
570 * Implemented native HTTP support in the BGZF library. Samtools is now
571 able to directly open a BAM file on HTTP. HTTP proxy is also
572 supported via the "http_proxy" environmental variable.
574 * Samtools is now compitable with the MinGW (win32) compiler and the
577 * The calmd (or fillmd) command now calculates the NM tag and replaces
578 MD tags if they are wrong.
580 * The view command now recognizes and optionally prints FLAG in HEXs or
581 strings to make a SAM file more friendly to human eyes. This is a
582 samtools-C extension, not implemented in Picard for the time
583 being. Please type `samtools view -?' for more information.
585 * BAM files now have an end-of-file (EOF) marker to facilitate
586 truncation detection. A warning will be given if an on-disk BAM file
587 does not have this marker. The warning will be seen on BAM files
588 generated by an older version of samtools. It does NO harm.
590 * New key bindings in tview: `r' to show read names and `s' to show
591 reference skip (N operation) as deletions.
593 * Fixed a bug in `samtools merge -n'.
595 * Samtools merge now optionally copies the header of a user specified
596 SAM file to the resultant BAM output.
598 * Samtools pileup/tview works with a CIGAR with the first or the last
599 operation is an indel.
601 * Fixed a bug in bam_aux_get().
604 Changes in other utilies:
606 * Fixed wrong FLAG in maq2sam.
609 (0.1.6: 2 September 2009, r453)
613 Beta Release 0.1.5 (7 July, 2009)
614 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
618 * Support opening a BAM alignment on FTP. Users can now use "tview" to
619 view alignments at the NCBI ftp site. Please read manual for more
622 * In library, propagate errors rather than exit or complain assertion
625 * Simplified the building system and fixed compiling errors caused by
628 * Fixed an issue about lost header information when a SAM is imported
631 * Implemented "samtool.pl varFilter" which filters both SNPs and short
632 indels. This command replaces "indelFilter".
634 * Implemented "samtools.pl pileup2fq" to generate FASTQ consensus from
637 * In pileup, cap mapping quality at 60. This helps filtering when
638 different aligners are in use.
640 * In pileup, allow to output variant sites only.
642 * Made pileup generate correct calls in repetitive region. At the same
643 time, I am considering to implement a simplified model in SOAPsnp,
644 although this has not happened yet.
646 * In view, added '-u' option to output BAM without compression. This
647 option is preferred when the output is piped to other commands.
649 * In view, added '-l' and '-r' to get the alignments for one library or
650 read group. The "@RG" header lines are now partially parsed.
652 * Do not include command line utilities to libbam.a.
654 * Fixed memory leaks in pileup and bam_view1().
656 * Made faidx more tolerant to empty lines right before or after FASTA >
660 Changes in other utilities:
662 * Updated novo2sam.pl by Colin Hercus, the key developer of novoalign.
665 This release involves several modifications to the key code base which
666 may potentially introduce new bugs even though we have tried to minimize
667 this by testing on several examples. Please let us know if you catch
670 (0.1.5: 7 July 2009, r373)
674 Beta Release 0.1.4 (21 May, 2009)
675 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
679 * Added the 'rmdupse' command: removing duplicates for SE reads.
681 * Fixed a critical bug in the indel caller: clipped alignments are not
684 * Fixed a bug in the tview: gapped alignment may be incorrectly
687 * Unified the interface to BAM and SAM I/O. This is done by
688 implementing a wrapper on top of the old APIs and therefore old APIs
689 are still valid. The new I/O APIs also recognize the @SQ header
692 * Generate the MD tag.
694 * Generate "=" bases. However, the indel caller will not work when "="
697 * Enhanced support of color-read display (by Nils Homer).
699 * Implemented the GNU building system. However, currently the building
700 system does not generate libbam.a. We will improve this later. For
701 the time being, `make -f Makefile.generic' is preferred.
703 * Fixed a minor bug in pileup: the first read in a chromosome may be
706 * Fixed bugs in bam_aux.c. These bugs do not affect other components as
707 they were not used previously.
709 * Output the 'SM' tag from maq2sam.
711 (0.1.4: 21 May 2009, r297)
715 Beta Release 0.1.3 (15 April, 2009)
716 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
718 Notable changes in SAMtools:
720 * SAMtools is more consistent with the specification: a) '*' in the
721 QUAL field is allowed; b) the field separator is TAB only and SPACE
722 is treated as a character in a field; c) empty header is allowed.
724 * Implemented GLFv3 support in pileup.
726 * Fixed a severe bug in fixmate: strand information is wrongly
729 * Fixed a bug in alignment retrieval: alignments bridging n*16384bp are
730 not correctly retrieved sometimes.
732 * Fixed a bug in rmdup: segfault if unmapped reads are present.
734 * Move indel_filter.pl to samtools.pl and improved the filtering by
735 checking the actual number of alignments containing indels. The indel
736 pileup line is also changed a little to make this filtration easier.
738 * Fixed a minor bug in indexing: the bin number of an unmapped read is
741 * Added `flagstat' command to show statistics on the FLAG field.
743 * Improved indel caller by setting the maximum window size in local
746 Changes in other utilities:
748 * Fixed a bug in maq2sam: a tag name is obsolete.
750 * Improvement to wgsim: a) added support for SOLiD read simulation; b)
751 show the number of substitutions/indels/errors in read name; c)
752 considerable code clean up.
754 * Various converters: improved functionality in general.
756 * Updated the example SAM due to the previous bug in fixmate.
758 (0.1.3: 15 April 2009, r227)
762 Beta Release 0.1.2 (28 January, 2008)
763 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
765 Notable changes in SAMtools:
767 * Implemented a Bayesian indel caller. The new caller generate scores
768 and genotype and is potentially more accurate than Maq's indel
769 caller. The pileup format is also changed accordingly.
771 * Implemented rmdup command: remove potential PCR duplicates. Note that
772 this command ONLY works for FR orientation and requires ISIZE is
775 * Added fixmate command: fill in mate coordinates, ISIZE and mate
776 related flags from a name-sorted alignment.
778 * Fixed a bug in indexing: reads bridging 16x kbp were not retrieved.
780 * Allow to select reads shown in the pileup output with a mask.
782 * Generate GLFv2 from pileup.
784 * Added two more flags for flagging PCR/optical duplicates and for QC
787 * Fixed a bug in sort command: name sorting for large alignment did not
790 * Allow to completely disable RAZF (using Makefile.lite) as some people
791 have problem to compile it.
793 * Fixed a bug in import command when there are reads without
796 * Fixed a bug in tview: clipping broke the alignment viewer.
798 * Fixed a compiling error when _NO_CURSES is applied.
800 * Fixed a bug in merge command.
802 Changes in other utilities:
804 * Added wgsim, a paired-end reads simulator. Wgsim was adapted from
805 maq's reads simulator. Colin Hercus further improved it to allow
808 * Added wgsim_eval.pl, a script that evaluates the accuracy of
809 alignment on reads generated by wgsim.
811 * Added soap2sam.pl, a SOAP2->SAM converter. This converter does not
812 work properly when multiple hits are output.
814 * Added bowtie2sam.pl, a Bowtie->SAM converter. Only the top hit will
815 be retained when multiple hits are present.
817 * Fixed a bug in export2sam.pl for QC reads.
819 * Support RG tag at MAQ->SAM converter.
821 * Added novo2sam.pl, a NovoAlign->SAM converter. Multiple hits and
822 indel are not properly handled, though.
824 * Added zoom2sam.pl, a ZOOM->SAM converter. It only works with the
825 default Illumina output.
827 (0.1.2: 28 January 2008; r116)
831 Beta Release 0.1.1 (22 December, 2008)
832 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
834 The is the first public release of samtools. For more information,
835 please check the manual page `samtools.1' and the samtools website
836 http://samtools.sourceforge.net