+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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* 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
+ 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
projects / samtools.git / blobdiff