What's new in SAM Tools 1.2.1
Feb 5, 2015
- The 1.2.1 release of HTSlib and the 1.2 releases of Samtools and BCFtools provide substantial improvements in CRAM support and variant calling, as well as a number of bug fixes and speed improvements. (The 1.2 HTSlib release was immediately superseded by 1.2.1 when a compatibilty issue with previous HTSlib releases was identified.)
- NOTEWORTHY CHANGES IN SAMTOOLS:
- flagstat now works on SAM, BAM, or CRAM files (rather than BAM only)
- stats calculates mismatches per cycle for unclipped length
- merge can now merge SAM input files
- CRAM reference files are now cached by default (see HTSlib below and samtools(1) man page)
- Tested against Intel-optimised zlib (https://github.com/jtkukunas/zlib; see README for details)
- Fixed bugs #302, #309, #318, and #327
- NOTEWORTHY CHANGES IN BCFTOOLS:
- new consensus command
- new annotate plugins: fixploidy, vcf2sex, tag2tag
- more features in convert command, amongst others new --hapsample function (thanks to Warren Kretzschmar)
- support for complements in bcftools annotate --remove
- support for -i/-e filtering expressions in isec
- improved error reporting
- call command changes:
- the default prior increased from -P1e-3 to -P1.1e-3, some clear calls were missed with default settings previously
- support for the new symbolic allele
- support for -f GQ
- bug fixes, such as: proper trimming of DPR tag with -c; the -A switch does not add back records removed by -v and the behaviour has been made consistent with -c and -m
- many bug fixes and improvements, such as
- bug in filtering, FMT & INFO vs INFO & FMT
- fixes in bcftools merge
- filter update AN/AC with -S
- isec outputs matching records for both VCFs in the Venn mode
- annotate considers alleles when working with Number=A,R tags
- new --set-id feature for annotate
- convert can be used similarly to view
- NOTEWORTHY CHANGES IN HTSLIB:
- HTSlib now has a configure script which checks your build environment and allows for selection of optional extras. See INSTALL for details
- By default, reference sequences are fetched from the EBI CRAM Reference Registry and cached in your $HOME cache directory. This behaviour can be controlled by setting REF_PATH and REF_CACHE enviroment variables (see the samtools(1) man page for details)
- Numerous CRAM improvements:
- Support for CRAM v3.0, an upcoming revision to CRAM supporting better compression and per-container checksums
- EOF checking for v2.1 and v3.0 (similar to checking BAM EOF blocks)
- Non-standard values for PNEXT and TLEN fields are now preserved
- hts_set_fai_filename() now provides a reference file when encoding
- Generated read names are now numbered from 1, rather than being labelled slice:record-in-slice
- Multi-threading and speed improvements
- New htsfile command for identifying file formats, and corresponding file format detection APIs
- New tabix --regions FILE, --targets FILE options for filtering via BED files
- Optional iRODS file access, disabled by default. Configure with --with-irods to enable accessing iRODS data objects directly via irods:DATAOBJ
- All occurences of 2^29 in the source have been eliminated, so indexing and querying against reference sequences larger than 512Mbp works (when using CSI indices)
- Support for plain GZIP compression in various places
- VCF header editing speed improvements
- Added seq_nt16_int[] (equivalent to the samtools API's bam_nt16_nt4_table[])
- Reinstated faidx_fetch_nseq(), which was accidentally removed from 1.1. Now faidx_fetch_nseq() and faidx_nseq() are equivalent; eventually faidx_fetch_nseq() will be deprecated and removed [#156]
- Reinstated hts_file_type() and FT_* macros, which were available until 1.1 but briefly removed in 1.2. This function is deprecated and will be removed in a future release—you should use hts_detect_format() etc instead
- Fixed bugs #141, #152, #155, #158, #159, and various memory leaks
New in SAM Tools 1.1 (Sep 24, 2014)
- Samtools fixmate and flagstat now consider supplementary reads
- Sorting BAM files with thousands of reference contigs now completes in a reasonable amount of time (#260)
- Fixed samtools idxstats when displaying statistics from indices generated by samtools 0.1.x (#124)
- Fixed samtools calmd memory leak (#143)
- Samtools fixmate now only adds a template cigar tag (ct:Z) when requested with -c, and never adds it repeatedly (#276)
- Regularised script #! directives as #!/usr/bin/env perl etc (#271, #273)
- Fixed DPR annotation in samtools mpileup
- New bcftools convert and plugin commands and annotate --rename-chrs option
- BCFtools norm performance is improved and now averages QUALs and accumulates IDs and FILTERs
- Improved bcftools filter expressions, query support for IUPAC ambiguity codes, and annotate support for genotype fields
- Plugins for bcftools have now moved from annotate to the new plugin command
New in SAM Tools 1.0 Beta (Aug 16, 2014)
- Added support for the CRAM sequencing file format.
New in SAM Tools 0.1.19 Beta (Mar 15, 2013)
- Many important bugfixes and contributions by many people. Thanks to all!
- Performance improvements (multi-threading)
- Important changes in calling
- New annotations useful for filtering (RPB, HWE, QBD, MDV)
- New tools, bamcheck and plot-bamcheck
- New features in samtools tview
New in SAM Tools 0.1.18 Beta (Sep 9, 2011)
- fixed a bug in phase (due to recent changes)
- fixed a bug in vcf2fq
New in SAM Tools 0.1.15 Beta (Apr 11, 2011)
- 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.
New in SAM Tools 0.1.9 (Oct 28, 2010)
- Changes to the pileup format. A reference skip (the N CIGAR operator)
- is shown as '' 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.
New in SAM Tools 0.1.3 (May 11, 2009)
- 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.