CAVA Upgraded!

In this release, we've switched to supporting CAVAv1.2 instead of previous versions. This is because CAVAv1.1 would incorrectly notate certain multi-exon UTR variants. Since the authors changed the database format, we will only support v1.2+ moving forward.

Other fixes include:

• Removed a bug that always included HTML Links in the info field
• added more default parameters to vt to quiet it down more.
• removed bior_overlap examples from the catalog and drill files (I don't use them anymore)

Minor fixes to SNPEff table output

The generated tsv file failed to pull the correct headers from SNPEff due to a version change. This has now been fixed.

Version 3.0

This release causes breaking changes due to CAVA upgrades. It will only work with CAVA 1.2+ because the database and output formats have changed.

Other notable changes:

• By default, bior_annotate will not remove duplicate entries based on chrom, pos, ref, and alt. If you still want to use this feature (discouraged), you can set the -u option.
• Changed default to be less verbose from VT
• Changed default behavior to run in standalone mode, rather than SGE cluster
• Redirected STDERR and STDOUT to file during tests.

SNPEff fix-pack

This release has multiple fixes to support SNPEff, and it also filters out the ##SAMPLE column that can cause issues downstream with old versions of BioR.

Updates BioR Config Path

v2.8.6

Updated bior version

v2.8.5

This release includes:

• Several enhancements to the Docker deployment, including tutorial
• A bugfix in the CompoundHet script that was missing certain types of variants
• Now includes vt normalization (new config requirement)
• Changed code to allow bgzipped VCF files with *bgz extension
• General bugfixes

Pre-paper release

Release candidate version.