* optionally drop phase ambiguous reads

[samtools.git] / NEWS

Beta release 0.1.13 (28 February, 2011)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The most important though largely invisible modification is the change of the
order of genotypes in the PL VCF/BCF tag. This is to conform the upcoming VCF
spec v4.1. The change means that 0.1.13 is not backward compatible with VCF/BCF
generated by samtools older than r921 inclusive.  VCF/BCF generated by the new
samtools will contain a line `##fileformat=VCFv4.1' as well as the samtools
version number.

Single Individual Haplotyping (SIH) is added as an experimental feature. It
originally aims to produce haploid consensus from fosmid pool sequencing, but
also works with short-read data. For short reads, phased blocks are usually too
short to be useful in most applications, but phasing can be powerful for ruling
out some SNPs close to INDELs and some of clustered spurious SNPs between copies
of CNVs. On one data set, phasing based SNP calling is better in terms of both
sensitivity and specificity than the standard methods.


Other notable changes in samtools:

 * Construct per-sample consensus to reduced the effect of nearby SNPs in INDEL
   calling. This may reduce the power, but improves specificity.

 * Improved sorting order checking in indexing. Now indexing is the preferred way
   to check if a BAM is sorted.

 * Added a switch `-E' to mpileup and calmd. This option uses an alternative way
   to apply BAQ, which increases sensistivity, especially to MNPs, at the cost of
   a little loss in specificity.

 * Added `mpileup -A' to allow to use reads in anomalous pairs in SNP calling.

 * Added `mpileup -m' to allow fine control of INDEL candidates.

 * Added `mpileup -S' to compute per-sample strand bias P-value.

 * Added `mpileup -G' to exclude read groups in variant calling.

 * Fixed segfault in indel calling related to unmapped and refskip reads.

 * Fixed an integer overflow in INDEL calling. This bug produces wrong INDEL
   genotypes for longer INDELs, typically over 10bp.

 * Fixed a bug in tview on big-endian machines.

 * Fixed a very rare memory issue in bam_md.c

 * Fixed an out-of-boundary bug in mpileup when the read base is `N'.

 * Fixed a compiling error when the knetfile library is not used. Fixed a
   library compiling error due to the lack of bam_nt16_nt4_table[] table.


Other notable changes in bcftools:

 * Updated the BCF spec.

 * Added the `FQ' VCF INFO field, which gives the phred-scaled probability
   of all samples being the samei (identical to the reference or all homozygous
   variants). Option `view -f' has been dropped.

 * Implementated of "vcfutils.pl vcf2fq" to generate a consensus sequence
   similar to "samtools.pl pileup2fq".

 * Make sure the GT FORMAT field is always the first FORMAT to conform the VCF
   spec. Drop bcf-fix.pl.

 * Output bcftools specific INFO and FORMAT in the VCF header.

 * Added `view -s' to call variants from a subset of samples.

 * Properly convert VCF to BCF with a user provided sequence dictionary. Nonetheless,
   custom fields are still unparsed and will be stored as a missing value.

 * Fixed a minor bug in Fisher's exact test; the results are rarely changed.


(0.1.13: 28 February 2011, r926+130)



Beta release 0.1.12a (2 December, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This is another bug fix release:

 * Fixed a memory violation in mpileup, which causes segfault. Release
   0.1.9 and above are affected.

 * Fixed a memory violation in the indel caller, which does not causes
   segfault, but may potentially affect deletion calls in an unexpected
   way. Release 0.1.10 and above are affected.

 * Fixed a bug in computing r-square in bcftools. Few are using this
   functionality and it only has minor effect.

 * Fixed a memory leak in bam_fetch().

 * Fixed a bug in writing meta information to the BAM index for the last
   sequence. This bug is invisible to most users, but it is a bug anyway.

 * Fixed a bug in bcftools which causes false "DP4=0,0,0,0" annotations.

(0.1.12: 2 December 2010, r862)



Beta release 0.1.11 (21 November, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This is mainly a bug fix release:

 * Fixed a bug in random retrieval (since 0.1.8). It occurs when reads
   are retrieved from a small region containing no reads.

 * Fixed a bug in pileup (since 0.1.9). The bug causes an assertion
   failure when the first CIGAR operation is a deletion.

 * Improved fault tolerence in remote access.

One minor feature has been implemented in bcftools:

 * Added a reference-free variant calling mode. In this mode, a site is
   regarded as a variat iff the sample(s) contains two or more alleles;
   the meaning of the QUAL field in the VCF output is changed
   accordingly. Effectively, the reference allele is irrelevant to the
   result in the new mode, although the reference sequence has to be
   used in realignment when SAMtools computes genotype likelihoods.

In addition, since 0.1.10, the `pileup' command has been deprecated by
`mpileup' which is more powerful and more accurate. The `pileup' command
will not be removed in the next few releases, but new features will not
be added.

(0.1.11: 21 November 2010, r851)



Beta Release 0.1.10 (16 November, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This release is featured as the first major improvement to the indel
caller. The method is similar to the old one implemented in the pileup
command, but the details are handled more carefully both in theory and
in practice. As a result, the new indel caller usually gives more
accurate indel calls, though at the cost of sensitivity. The caller is
implemented in the mpileup command and is invoked by default. It works
with multiple samples.

Other notable changes:

 * With the -r option, the calmd command writes the difference between
   the original base quality and the BAQ capped base quality at the BQ
   tag but does not modify the base quality. Please use -Ar to overwrite
   the original base quality (the 0.1.9 behavior).

 * Allow to set a maximum per-sample read depth to reduce memory. In
   0.1.9, most of memory is wasted for the ultra high read depth in some
   regions (e.g. the chr1 centromere).

 * Optionally write per-sample read depth and per-sample strand bias
   P-value.

 * Compute equal-tail (Bayesian) credible interval of site allele
   frequency at the CI95 VCF annotation.

 * Merged the vcfutils.pl varFilter and filter4vcf for better SNP/indel
   filtering.

(0.1.10: 16 November 2010, r829)



Beta Release 0.1.9 (27 October, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This release is featured as the first major improvement to the samtools'
SNP caller.  It comes with a revised MAQ error model, the support of
multi-sample SNP calling and the computation of base alignment quality
(BAQ).

The revised MAQ error model is based on the original model. It solves an
issue of miscalling SNPs in repetitive regions. Althought such SNPs can
usually be filtered at a later step, they mess up unfiltered calls. This
is a theoretical flaw in the original model. The revised MAQ model
deprecates the orginal MAQ model and the simplified SOAPsnp model.

Multi-sample SNP calling is separated in two steps. The first is done by
samtools mpileup and the second by a new program, bcftools, which is
included in the samtools source code tree. Multi-sample SNP calling also
works for single sample and has the advantage of enabling more powerful
filtration. It is likely to deprecate pileup in future once a proper
indel calling method is implemented.

BAQ is the Phred-scaled probability of a read base being wrongly
aligned. Capping base quality by BAQ has been shown to be very effective
in suppressing false SNPs caused by misalignments around indels or in
low-complexity regions with acceptable compromise on computation
time. This strategy is highly recommended and can be used with other SNP
callers as well.

In addition to the three major improvements, other notable changes are:

 * Changes to the pileup format. A reference skip (the N CIGAR operator)
   is shown as '<' or '>' depending on the strand. Tview is also changed
   accordingly.

 * Accelerated pileup. The plain pileup is about 50% faster.

 * Regional merge. The merge command now accepts a new option to merge
   files in a specified region.

 * Fixed a bug in bgzip and razip which causes source files to be
   deleted even if option -c is applied.

 * In APIs, propogate errors to downstream callers and make samtools
   return non-zero values once errors occur.

(0.1.9: 27 October 2010, r783)



Beta Release 0.1.8 (11 July, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable functional changes:

 * Added the `reheader' command which replaces a BAM header with a new
   header. This command is much faster than replacing header by
   BAM->SAM->BAM conversions.

 * Added the `mpileup' command which computes the pileup of multiple
   alignments.

 * The `index' command now stores the number of mapped and unmapped
   reads in the index file. This information can be retrieved quickly by
   the new `idxstats' command.

 * By default, pileup used the SOAPsnp model for SNP calling. This
   avoids the floating overflow in the MAQ model which leads to spurious
   calls in repetitive regions, although these calls will be immediately
   filtered by varFilter.

 * The `tview' command now correctly handles CIGARs like 7I10M and
   10M1P1I10M which cause assertion failure in earlier versions.

 * Tview accepts a region like `=10,000' where `=' stands for the
   current sequence name. This saves typing for long sequence names.

 * Added the `-d' option to `pileup' which avoids slow indel calling
   in ultradeep regions by subsampling reads locally.

 * Added the `-R' option to `view' which retrieves alignments in read
   groups listed in the specified file.

Performance improvements:

 * The BAM->SAM conversion is up to twice faster, depending on the
   characteristic of the input.

 * Parsing SAM headers with a lot of reference sequences is now much
   faster.

 * The number of lseek() calls per query is reduced when the query
   region contains no read alignments.

Bug fixes:

 * Fixed an issue in the indel caller that leads to miscall of indels.
   Note that this solution may not work well when the sequencing indel
   error rate is higher than the rate of SNPs.

 * Fixed another issue in the indel caller which may lead to incorrect
   genotype.

 * Fixed a bug in `sort' when option `-o' is applied.

 * Fixed a bug in `view -r'.

APIs and other changes:

 * Added iterator interfaces to random access and pileup. The callback
   interfaces directly call the iterator interfaces.

 * The BGZF blocks holding the BAM header are indepedent of alignment
   BGZF blocks. Alignment records shorter than 64kB is guaranteed to be
   fully contained in one BGZF block. This change is fully compatible
   with the old version of samtools/picard.

Changes in other utilities:

 * Updated export2sam.pl by Chris Saunders.

 * Improved the sam2vcf.pl script.

 * Added a Python version of varfilter.py by Aylwyn Scally.

(0.1.8: 11 July 2010, r613)



Beta Release 0.1.7 (10 November, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes:

 * Improved the indel caller in complex scenariors, in particular for
   long reads. The indel caller is now able to make reasonable indel
   calls from Craig Venter capillary reads.

 * Rewrote single-end duplicate removal with improved
   performance. Paired-end reads are not touched.

 * Duplicate removal is now library aware. Samtools remove potential
   PCR/optical dupliates inside a library rather than across libraries.

 * SAM header is now fully parsed, although this functionality is not
   used in merging and so on.

 * In samtools merge, optionally take the input file name as RG-ID and
   attach the RG tag to each alignment.

 * Added FTP support in the RAZF library. RAZF-compressed reference
   sequence can be retrieved remotely.

 * Improved network support for Win32.

 * Samtools sort and merge are now stable.

Changes in other utilities:

 * Implemented sam2vcf.pl that converts the pileup format to the VCF
   format.

 * This release of samtools is known to work with the latest
   Bio-Samtools Perl module.

(0.1.7: 10 November 2009, r510)



Beta Release 0.1.6 (2 September, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes:

 * In tview, do not show a blank screen when no reads mapped to the
   corresponding region.

 * Implemented native HTTP support in the BGZF library. Samtools is now
   able to directly open a BAM file on HTTP. HTTP proxy is also
   supported via the "http_proxy" environmental variable.

 * Samtools is now compitable with the MinGW (win32) compiler and the
   PDCurses library.

 * The calmd (or fillmd) command now calculates the NM tag and replaces
   MD tags if they are wrong.

 * The view command now recognizes and optionally prints FLAG in HEXs or
   strings to make a SAM file more friendly to human eyes. This is a
   samtools-C extension, not implemented in Picard for the time
   being. Please type `samtools view -?' for more information.

 * BAM files now have an end-of-file (EOF) marker to facilitate
   truncation detection. A warning will be given if an on-disk BAM file
   does not have this marker. The warning will be seen on BAM files
   generated by an older version of samtools. It does NO harm.

 * New key bindings in tview: `r' to show read names and `s' to show
   reference skip (N operation) as deletions.

 * Fixed a bug in `samtools merge -n'.

 * Samtools merge now optionally copies the header of a user specified
   SAM file to the resultant BAM output.

 * Samtools pileup/tview works with a CIGAR with the first or the last
   operation is an indel.

 * Fixed a bug in bam_aux_get().


Changes in other utilies:

 * Fixed wrong FLAG in maq2sam.


(0.1.6: 2 September 2009, r453)



Beta Release 0.1.5 (7 July, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes:

 * Support opening a BAM alignment on FTP. Users can now use "tview" to
   view alignments at the NCBI ftp site. Please read manual for more
   information.

 * In library, propagate errors rather than exit or complain assertion
   failure.

 * Simplified the building system and fixed compiling errors caused by
   zlib<1.2.2.1.

 * Fixed an issue about lost header information when a SAM is imported
   with "view -t".

 * Implemented "samtool.pl varFilter" which filters both SNPs and short
   indels. This command replaces "indelFilter".

 * Implemented "samtools.pl pileup2fq" to generate FASTQ consensus from
   pileup output.

 * In pileup, cap mapping quality at 60. This helps filtering when
   different aligners are in use.

 * In pileup, allow to output variant sites only.

 * Made pileup generate correct calls in repetitive region. At the same
   time, I am considering to implement a simplified model in SOAPsnp,
   although this has not happened yet.

 * In view, added '-u' option to output BAM without compression. This
   option is preferred when the output is piped to other commands.

 * In view, added '-l' and '-r' to get the alignments for one library or
   read group. The "@RG" header lines are now partially parsed.

 * Do not include command line utilities to libbam.a.

 * Fixed memory leaks in pileup and bam_view1().

 * Made faidx more tolerant to empty lines right before or after FASTA >
   lines.


Changes in other utilities:

 * Updated novo2sam.pl by Colin Hercus, the key developer of novoalign.


This release involves several modifications to the key code base which
may potentially introduce new bugs even though we have tried to minimize
this by testing on several examples. Please let us know if you catch
bugs.

(0.1.5: 7 July 2009, r373)



Beta Release 0.1.4 (21 May, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes:

 * Added the 'rmdupse' command: removing duplicates for SE reads.

 * Fixed a critical bug in the indel caller: clipped alignments are not
   processed correctly.

 * Fixed a bug in the tview: gapped alignment may be incorrectly
   displayed.

 * Unified the interface to BAM and SAM I/O. This is done by
   implementing a wrapper on top of the old APIs and therefore old APIs
   are still valid. The new I/O APIs also recognize the @SQ header
   lines.

 * Generate the MD tag.

 * Generate "=" bases. However, the indel caller will not work when "="
   bases are present.

 * Enhanced support of color-read display (by Nils Homer).

 * Implemented the GNU building system. However, currently the building
   system does not generate libbam.a. We will improve this later. For
   the time being, `make -f Makefile.generic' is preferred.

 * Fixed a minor bug in pileup: the first read in a chromosome may be
   skipped.

 * Fixed bugs in bam_aux.c. These bugs do not affect other components as
   they were not used previously.

 * Output the 'SM' tag from maq2sam.

(0.1.4: 21 May 2009, r297)



Beta Release 0.1.3 (15 April, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes in SAMtools:

 * SAMtools is more consistent with the specification: a) '*' in the
   QUAL field is allowed; b) the field separator is TAB only and SPACE
   is treated as a character in a field; c) empty header is allowed.

 * Implemented GLFv3 support in pileup.

 * Fixed a severe bug in fixmate: strand information is wrongly
   overwritten.

 * Fixed a bug in alignment retrieval: alignments bridging n*16384bp are
   not correctly retrieved sometimes.

 * Fixed a bug in rmdup: segfault if unmapped reads are present.

 * Move indel_filter.pl to samtools.pl and improved the filtering by
   checking the actual number of alignments containing indels. The indel
   pileup line is also changed a little to make this filtration easier.

 * Fixed a minor bug in indexing: the bin number of an unmapped read is
   wrongly calculated.

 * Added `flagstat' command to show statistics on the FLAG field.

 * Improved indel caller by setting the maximum window size in local
   realignment.

Changes in other utilities:

 * Fixed a bug in maq2sam: a tag name is obsolete.

 * Improvement to wgsim: a) added support for SOLiD read simulation; b)
   show the number of substitutions/indels/errors in read name; c)
   considerable code clean up.

 * Various converters: improved functionality in general.

 * Updated the example SAM due to the previous bug in fixmate.

(0.1.3: 15 April 2009, r227)



Beta Release 0.1.2 (28 January, 2008)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes in SAMtools:

 * Implemented a Bayesian indel caller. The new caller generate scores
   and genotype and is potentially more accurate than Maq's indel
   caller. The pileup format is also changed accordingly.

 * Implemented rmdup command: remove potential PCR duplicates. Note that
   this command ONLY works for FR orientation and requires ISIZE is
   correctly set.

 * Added fixmate command: fill in mate coordinates, ISIZE and mate
   related flags from a name-sorted alignment.

 * Fixed a bug in indexing: reads bridging 16x kbp were not retrieved.

 * Allow to select reads shown in the pileup output with a mask.

 * Generate GLFv2 from pileup.

 * Added two more flags for flagging PCR/optical duplicates and for QC
   failure.

 * Fixed a bug in sort command: name sorting for large alignment did not
   work.

 * Allow to completely disable RAZF (using Makefile.lite) as some people
   have problem to compile it.

 * Fixed a bug in import command when there are reads without
   coordinates.

 * Fixed a bug in tview: clipping broke the alignment viewer.

 * Fixed a compiling error when _NO_CURSES is applied.

 * Fixed a bug in merge command.

Changes in other utilities:

 * Added wgsim, a paired-end reads simulator. Wgsim was adapted from
   maq's reads simulator. Colin Hercus further improved it to allow
   longer indels.

 * Added wgsim_eval.pl, a script that evaluates the accuracy of
   alignment on reads generated by wgsim.

 * Added soap2sam.pl, a SOAP2->SAM converter. This converter does not
   work properly when multiple hits are output.

 * Added bowtie2sam.pl, a Bowtie->SAM converter. Only the top hit will
   be retained when multiple hits are present.

 * Fixed a bug in export2sam.pl for QC reads.

 * Support RG tag at MAQ->SAM converter.

 * Added novo2sam.pl, a NovoAlign->SAM converter. Multiple hits and
   indel are not properly handled, though.

 * Added zoom2sam.pl, a ZOOM->SAM converter. It only works with the
   default Illumina output.

(0.1.2: 28 January 2008; r116)



Beta Release 0.1.1 (22 December, 2008)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The is the first public release of samtools. For more information,
please check the manual page `samtools.1' and the samtools website
http://samtools.sourceforge.net