X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=NEWS;h=1aa23593df188b1827f6e46bf1779874552fd100;hp=946ba7b4e98d584081b846105bde5f438f6e3ba1;hb=5075acdfc387c56ca8411cde3e419e867da9804d;hpb=6828a9a9ef02c5634d488a3b3a52966a92d38088 diff --git a/NEWS b/NEWS index 946ba7b..1aa2359 100644 --- a/NEWS +++ b/NEWS @@ -1,4 +1,118 @@ -Beta release 0.1.14 (16 March, 2011) +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 @@ -9,17 +123,41 @@ 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. +ploidy of each sample (see also manual bcftools/bcftools.1). + +Other notable changes: -Other new features: + * 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. - * Added `bcftools view -F' to parse BCF files generated by samtools r921 or - older which encode PL in a different way. + * Updated `misc/export2sam.pl', provided by Chris Saunders from Illumina Inc. -(0.1.14: 16 March 2011, r930:163) +(0.1.14: 21 March 2011, r933:170)