Tuesday, April 12, 2011

NEW SAM tools 0.1.15 @ SourceForge.net

Another new version of SAMtools - important new features here:
Also a new Tabix 0.2.4 with BED support !!!!

* 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)

(Via Download SAM tools from SourceForge.net.)