X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=NEWS;h=41a6cc8ebe05185ea8e97f0639fede7ce15675d9;hp=6b4d8aac5ede779b7efee6e02969dea40926275c;hb=b990d9d3dd518a9cf7b7f4a165c584d8d8d1cfb0;hpb=f2f3968e11eead9ce5601b01890bc2339ff951e9 diff --git a/NEWS b/NEWS index 6b4d8aa..41a6cc8 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,274 @@ +Beta Release 0.1.18 (2 September, 2011) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Notable changes in samtools: + + * Support the new =/X CIGAR operators (by Peter Cock). + + * Allow to subsample BAM while keeping the pairing intact (view -s). + + * Implemented variant distance bias as a new filter (by Petr Danecek). + + * Bugfix: huge memory usage during indexing + + * Bugfix: use of uninitialized variable in mpileup (rare) + + * Bugfix: wrong BAQ probability (rare) + +Notable changes in bcftools: + + * Support indel in the contrast caller. + + * Bugfix: LRT2=nan in rare cases + +(0.1.18: 2 September 2011, r982:295) + + + +Beta Release 0.1.17 (6 July, 2011) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +With the maturity of `mpileup' and the lack of update in the `pileup' command, +the `pileup' command is now formally dropped. Most of the pileup functionality, +such as outputting mapping quality and read positions, have been added +`mpileup'. + +Since this release, `bcftools view' is able to perform contrast SNP calling +(option -T) for discovering de novo and/or somatic mutations between a pair of +samples or in a family trio. Potential mutations are scored by a log likelihood +ratio, which is very simple in math, but should be comparable to more +sophisticated methods. Note that getting the score is only the very first step. +A lot more need to be done to reduce systematical errors due to mapping and +reference errors and structural variations. + +Other notable changes in samtools: + + * Improved sorting order checking during indexing. + + * Improved region parsing. Colons in reference sequence names are parsed + properly. + + * Fixed an issue where mpileup does not apply BAQ for the first few reads when + a region is specified. + + * Fixed an issue where `faidx' does not work with FASTA files with long lines. + + * Bugfix: wrong SP genotype information in the BCF output. + +Other notable changes in bcftools: + + * Output the ML esitmate of the allele count. + + * Added the HWE plus F<0 filter to varFilter. For multiple samples, it + effectively filters false heterozygous calls around centromeres. + + * For association mapping, perform both 1-degree and 2-degree test. The + 2-degree test is conservative but more robust to HWE violation. + +(0.1.17: 6 July 2011, r973:277) + + + +Beta Release 0.1.16 (21 April, 2011) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Notable changes in samtools: + + * Support the new SAM/BAM type `B' in the latest SAM spec v1.4. + + * When the output file of `samtools merge' exists, do not overwrite it unless + a new command-line option `-f' is applied. + + * Bugfix: BED support is not working when the input BED is not sorted. + + * Bugfix: some reads without coordinates but given on the reverse strand are + lost in merging. + +Notable changes in bcftools: + + * Code cleanup: separated max-likelihood inference and Bayesian inference. + + * Test Hardy-Weinberg equilibrium with a likelihood-ratio test. + + * Provided another association test P-value by likelihood-ratio test. + + * Use Brent's method to estimate the site allele frequency when EM converges + slowly. The resulting ML estimate of allele frequnecy is more accurate. + + * Added the `ldpair' command, which computes r^2 between SNP pairs given in + an input file. + +Also, the `pileup' command, which has been deprecated by `mpileup' since +version 0.1.10, will be dropped in the next release. The old `pileup' command +is substandard and causing a lot of confusion. + +(0.1.16: 21 April 2011, r963:234) + + + +Beta Release 0.1.15 (10 April, 2011) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Noteable changes: + + * Allow to perform variant calling or to extract information in multiple + regions specified by a BED file (`samtools mpileup -l', `samtools view -L' + and `bcftools view -l'). + + * Added the `depth' command to samtools to compute the per-base depth with a + simpler interface. File `bam2depth.c', which implements this command, is the + recommended example on how to use the mpileup APIs. + + * Estimate genotype frequencies with ML; perform chi^2 based Hardy-Weinberg + test using this estimate. + + * For `samtools view', when `-R' is specified, drop read groups in the header + that are not contained in the specified file. + + * For `samtools flagstat', separate QC-pass and QC-fail reads. + + * Improved the command line help of `samtools mpileup' and `bcftools view'. + + * Use a global variable to control the verbose level of samtools stderr + output. Nonetheless, it has not been full utilized. + + * Fixed an issue in association test which may report false associations, + possibly due to floating point underflow. + +(0.1.15: 10 April 2011, r949:203) + + + +Beta release 0.1.14 (21 March, 2011) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +This release implements a method for testing associations for case-control +data. The method does not call genotypes but instead sums over all genotype +configurations to compute a chi^2 based test statistics. It can be potentially +applied to comparing a pair of samples (e.g. a tumor-normal pair), but this +has not been evaluated on real data. + +Another new feature is to make X chromosome variant calls when female and male +samples are both present. The user needs to provide a file indicating the +ploidy of each sample (see also manual bcftools/bcftools.1). + +Other notable changes: + + * Added `bcftools view -F' to parse BCF files generated by samtools r921 or + older which encodes PL in a different way. + + * Changed the behavior of `bcftools view -s'. Now when a list of samples is + provided, the samples in the output will be reordered to match the ordering + in the sample list. This change is mainly designed for association test. + + * Sped up `bcftools view -v' for target sequencing given thousands of samples. + Also added a new option `view -d' to skip loci where only a few samples are + covered by reads. + + * Dropped HWE test. This feature has never been implemented properly. An EM + should be much better. To be implemented in future. + + * Added the `cat' command to samtools. This command concatenate BAMs with + identical sequence dictionaries in an efficient way. Modified from bam_cat.c + written by Chris Saunders. + + * Added `samtools view -1' to write BAMs at a low compression level but twice + faster to create. The `sort' command generates temporary files at a low + compression level as well. + + * Added `samtools mpileup -6' to accept "BAM" with Illumina 1.3+ quality + strings (strictly speaking, such a file is not BAM). + + * Added `samtools mpileup -L' to skip INDEL calling in regions with + excessively high coverage. Such regions dramatically slow down mpileup. + + * Updated `misc/export2sam.pl', provided by Chris Saunders from Illumina Inc. + +(0.1.14: 21 March 2011, r933:170) + + + +Beta release 0.1.13 (1 March, 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 many applications, but they can help to rule out part of +SNPs close to INDELs or between copies of CNVs. + + +Other notable changes in samtools: + + * Construct per-sample consensus to reduce the effect of nearby SNPs in INDEL + calling. This reduces 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 the collection 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 short 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. + Suppress a compiling warning related to the latest zlib. + + +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 same (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: 1 March 2011, r926:134) + + + Beta release 0.1.12a (2 December, 2010) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -532,4 +803,4 @@ 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 \ No newline at end of file +http://samtools.sourceforge.net