Download

Using an existing thesaurus

As a thesaurus table file can be computationally intensive to create, you may wish to download and use an existing table.

Download

A thesaurus table for the whole human exome (hg19, Gencode V19 exonic regions and 1kb flanking regions) are available for download.

Reorder

The ordering of chromosomes in the thesaurus table must match exactly the order used in your VCF and BAM files. To make sure of this, you can re-order a downloaded thesaurus table before first use. The command for this is

java -jar GeneticThesaurus.jar reorder
    --verbose 
    --genome your.genome.fa
    --thesaurus downloaded.thesaurus.tsv.gz     
    --output thesaurus.tsv.gz

Reordering can take a long time and will create several large temporary files, so make sure there is ample free disk space (at least as much free as taken up by the original thesaurus file).