Preparing CHASMplus database for annotation


Hi all,

I want to use CHASMplus for annotation of my VCF files by ANNOVAR tool and I should reformat it to standard ANNOVAR genericDB format (Chr, Start, End, Ref, Alt, and other information), but I don't know how can I download this database. Can I do it at all?

Thanks for any help.






It is quite easy to annotate variants with CHASMplus scores by using OpenCRAVAT ( ), either by the webserver or command line tool. I assume, though, that you likely have an existing pipeline using ANNOVAR and would like to annotate with it for consistency.

You can alway access the data underlying an annotator in OpenCRAVAT, including CHASMplus. Basically what you need to do is to install OpenCRAVAT, download the CHASMplus annotator, and then dump the CHASMplus sqlite database file to a CSV file. You could then reformat the data to what ever is needed. Commands would look like the following:

# install OpenCRAVAT with CHASMplus annotator
pip install open-cravat
oc module install-base
oc module install -y chasmplus

# change directory to installed chasmplus data
cd `oc config md`/annotators/chasmplus/data/

# dump all sqlite tables to csv files
for t in chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chrX chrY transcript; do
    sqlite3 -header -csv chasmplus.sqlite "SELECT * FROM $t;" > `echo $t`.csv

before adding your answer.

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