vcfhacks v.0.1.16

vcfhacks v0.1.16

As well as the scripts precompiled executable versions of the scripts are now available for 64-bit Linux and Mac OS X. These binaries can be run without the need for installing perl modules on your machine.

If you prefer to download the scripts themselves download vcfhacks_scripts-0.1.16.zip. For the binary executables download vcfhacks_binaries-linux_0.1.16.tar.bz2 or vcfhacks_binaries-macosx_0.1.16.tar.bz2 depending on your OS. The two VEP plugins (SpliceConsensus.pm and SpliceConsensusFilter.pm) are available in a separate tarball for those that prefer to download the binary release.

Release Information

Several bugfixes and improvements:

-ensemblGeneAnnotator.pl now supports annotating RefSeq/Entrez IDs (i.e. if VEP was run using --refseq or --merged database options)

-ensemblGeneAnnotator.pl now supports use of SnpEff annotations (as long as -geneId flag was used when running snpEff)

-fixed an issue where files might be incorrectly interpreted as being bgzip compressed

-fixed an issue with filterVcfOnVcf.pl where a rogue progress message might print to STDOUT (and therefore appear in output if using > to redirect output rather than using -o option)

-fixed an issue with annovcfToSimple.pl where an extra column was added when using --summarise option without --contains_variant option

-ensured that INFO lines generated by annotateSnps.pl conform to VCF spec (i.e. GATK does not object to these lines anymore)

-additional modules are now moved into the lib subdirectory for tidyness

-URL for the github examples markdown file provided in readme

-progress bar in ensemblGeneAnnotator.pl is now optional with the --progress option

-updated pre-built ensemblGeneAnnotator database and made available as part of this release on github.