+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)
+
+
+