Releases: cancerit/BRASS
v3.0.4 - Sample name bugfix
Sanitise sample name corrected to permit .
v3.0.3 - bugfix release
Added support for empty results files
v3.0.2 - bug fix release
Fixed one bug:
Populate the platform field in options from the bam file
v3.0.1 - bug fix release
v3.0.0 - Data cleanup/enhancement
This release introduces some additional merging of events along with further early filtering which reduces runtime and false-calls.
The final results are enhanced in that:
- VCF file now has data for groups that failed to assemble included
- bedpe file is annotated and incorporates assembled data also
Although this is technically a duplication of output users have requested this.
v2.2.0 - relaxed header checking
Checking of the PL tag requires continual update to track SAM/BAM specification. Removed this check as there is no affect on downstream tools and a command line arg is available to force a value in resulting VCF files if necessary.
v2.1.1 - correct limit based processing
Number of required threads when using limit was not being set correctly. Generally results in needless thrashing of disk doing file checks but in some cases corrupt data or race conditions were occurring.
v2.1.0 - stabilises memory in assemble
Also improves sensitivity (more accurate insert size for BAMs with no MI tag) and specificity by excluding reads overlapping regions of high-depth (originally only groups completely contained in regions were excluded).
v2.0.1 - memory footprint
Improves memory footprint and runtime of brass-assemble step
v2.0.0 - First external release
Includes breakpoint refinement via assembly and verification of assembled reads.
When run via brass.pl there is a dependancy on grass for the annotation of events.
Be aware that the 'assembled' output doesn't include anything that hasn't assembled. We have plans to augment this output to include more events that can gain support from copy number information.