Bug fixes and improvements to SVrefine/SVbenchmark

A bug in previous versions of SVrefine was causing redundant VCF lines to be printed for some variants. This has been fixed. In addition, SVbenchmark was leaving temporary directories behind, and they are now correctly removed when no longer needed.

NOTE: SVbenchmark defaults for maximum distances between variants considered to be matches have been altered for more intuitive matching.

Bug fix/SVrefine

This version fixes a bug in SVrefine (introduced in v0.34) which broke SV detection when no --maxsize option was used. If you installed v0.34 and use SVrefine, please upgrade to v0.35 immediately.

Bug fix in SVrefine's variant region detection

In versions prior to v0.34, there was a bug in the way SVrefine detected regions potentially containing variants. This has now been fixed, resulting in better sensitivity in SVrefine structural variant detection.

New version of SVanalyzer--SVrefine now calls inversions

In this new version, SVbenchmark correctly performs comparison of non-sequence-specific deletions, so long as the ALT field for these deletions is "" and there is an END value specified in the INFO field.

In addition, inversion calling has now been added to SVrefine.

New options and bug fixes for SVmerge

This new version fixes a bug in SVmerge which was causing some singletons to be omitted from the clustered VCF output file. In addition, the new SVmerge option --seqspecific will omit SVs with no sequence specified for REF and ALT values (these variants are not generally clustered by SVmerge, so are printed as singletons).

Minor bug fixes and improvements in this revision

Critically, this release has working shebang lines in its scripts. In v0.3, user needs to call the scripts using "perl ".

New version of SVanalyzer

This version of SVanalyzer includes more informative logging and will be available for install through bioconda.

New options to SVbenchmark

This release includes new options for stringency of matching used in SVbenchmark, as well as the ability to require a minimum size of true variants when calculating recall and a minimum size of test variants when calculating precision. The release also includes SVrefine prediction of variants from minimap2 alignments (still beta).

Bug fix to SVrefine (--maxsize option) and SVcomp (output)

This release fixes bugs in SVrefine and SVcomp. Users should upgrade to this version immediately.

SVrefine now runs in "Discovery Mode"

This version was used for second round of SVrefine calls on the Genome in a Bottle Ashkenazi trio, uploaded on December 6, 2017.

In this version, SVrefine.pl can now be run in "discovery mode", without a BED file of regions, and it will report structural variants considering all instances of consistent, broken alignments between a query contig and the reference.