CAVA v1.2.0

Márton Münz

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Dec 21, 2016, 8:00:18 AM12/21/16

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A new version of our NGS variant annotation tool, CAVA v1.2.0 is available for download at www.icr.ac.uk/cava

In addition to important bug fixes, new features include:

- Improved transcript database generation tool

- Updated default transcript database to release 75 of Ensembl

- Additional outputted annotation flags

- Minor added features: prefix for annotation flags, protein length outputted

- Simple installation; no dependencies

- Source code is now also distributed on GitHub at https://github.com/RahmanTeam/CAVA

We would be grateful for any feedbacks or suggestions. Many thanks for your interest!

Hugues Sicotte

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Jan 6, 2017, 7:58:10 AM1/6/17

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Every one of those variants fails with a KeyError

if I use codon_usage=3 (they work if I use codon_usage=1)

I use a VERY simple (single gene) annotation

otherwise all other defaults in config file.

build37

I also pasted my tiny little ensembl file.

##fileformat=VCFv4.0

##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">

##FORMAT=<ID=AD,Number=2,Type=Integer,Description="Allele Depth">

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT DUMMYSAMPLE

22 42523460 22:42523460:G:A G A . PASS . AD:DP 941,200:1141

22 42523966 22:42523966:C:T C T . PASS . AD:DP 612,100:712

22 42524177 22:42524177:T:A T A . PASS . AD:DP 900,100:1000

22 42524244 22:42524244:T:C T C . PASS . AD:DP 900,100:1000

22 42522650 22:42522650:G:A G A . PASS . AD:DP 319,300:619

22 42524946 22:42524946:C:A C A . PASS . AD:DP 100,900:1000

22 42525086 22:42525086:A:C A C . PASS . AD:DP 990,100:1000

gunzip -c CYP2D6ensembl.gz

ENST00000360608 CYP2D6 ENSG00000100197 -/4.4kb/9/1.7kb/497 22 -1 42522500 42526908 116 42526793 42522576 42526613 42526908 42525739 42525911 42525034 42525187 42524785 42524946 42524175 42524352 42523843 42523985 42523448 42523636 42522852 42522994 42522500 42522754

Márton Münz

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Jan 6, 2017, 10:46:03 AM1/6/17

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Dear Hugues,

The @codon_usage option is not part of CAVA. If you are using a modification of CAVA which is not an official release, please contact the individual who provided you with your instance of CAVA.