v3.2.0: improves reference file generation

• Allows use of ensemblgenomes.org as a datasource
• Handle genes without names, and give more useful error message
• Ensure an error code is emmitted on failure

v3.1.1 - minor feature

Now possible to use AnnotateVcf.pl on a simple tsv file.

There must be entries for the 11 columns (header not needed)

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NORMAL  TUMOUR

These columns must be properly completed:

• CHROM
• POS
• REF
• ALT

All the other data columns can be ..

v3.0.0 - htslib upgrade / legacy removal

• Removed use of legacy Tabix codebase and switches to samtools 1.2+
• Switches to github version of vcftools and makes several patches unnecessary
• Several bugfixes

v2.1.2 - Update AnnotateVCF.pl for compatibility with wider range of algorithms

Minor update to remove algorithm specific dependancies when parsing VCF files. This should make AnnotateVcf.pl compatible with a wider variety of indel detection algorithms.

v2.1.1 - Minor changes to Admin script to cope with greater variety in Ensembl releases

Some minor changes to cope with changed Ensembl made to their FTP site file structure in more recent Ensembl releases.

v2.1.0 - Small feature update and some annotation improvements

Added a new option for AnnotateVcf.pl to zip and tabix index its results file.

Also improved the handling of some rarer transcript structures involving start and stop codons. Namely where the first base of a start codon was also the first base of an exon, or where the last base of a stop codon was the last base of an exon. Variants located close to start/stop codons in these structures should be handled more consistently now.

v2.0.0 - Fully decoupled from Ensembl DB

This is the first external release following a move to GitHub from internal repo and major rework to remove dependancy on an Ensembl database. Ensembl data files are still required for initial setup.

There is an outstanding edge case #1 that should be assessed by anyone using this version. The issue has no impact on grass which is the tool that has prompted this slightly early release for use in the PanCancer project.