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Releases: cancerit/BRASS

v3.0.4 - Sample name bugfix

23 Nov 11:32
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Sanitise sample name corrected to permit .

v3.0.3 - bugfix release

08 Sep 15:35
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Added support for empty results files

v3.0.2 - bug fix release

08 Jul 14:46
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Fixed one bug:
Populate the platform field in options from the bam file

v3.0.1 - bug fix release

07 Jul 19:50
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2 bugs corrected

  1. Error in VCF output for SVCLASS (#17) - inter-chromosomal events not correctly tagged as 'translocation'
  2. Version string in cpp programs (#18) - was being reported as ERSION rather than the actual value.

v3.0.0 - Data cleanup/enhancement

19 Jun 10:46
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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

30 Mar 10:02
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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

12 Mar 22:48
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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

16 Dec 06:19
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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

24 Nov 19:56
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Improves memory footprint and runtime of brass-assemble step

v2.0.0 - First external release

31 Oct 11:28
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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.