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getting_started.md

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Getting Started.

Installation

via bioconda

As a prerequisite, follow the bioconda getting started guide.

Then, create a new environment;

conda create -n mehari -y mehari
conda activate mehari

The mehari executable is now available from within the activated mehari conda environment:

mehari --help

via docker

Docker images of mehari are available from ghcr.io, see ghcr.io/varfish-org/mehari.

Downloading Prebuilt Databases

Annotating Example VCF Files

You can obtain an example file like this:

wget https://raw.githubusercontent.com/varfish-org/mehari/main/tests/data/db/create/seqvar_freqs/db-rs1263393206/input.vcf -O example.vcf

Now, annotate it using Mehari:

mehari annotate seqvars \
    --transcripts path/to/mehari-transcript-db \
    --frequencies path/to/mehari-frequency-db \
    --clinvar path/to/mehari-clinvar-db \
    --path-input-vcf example.vcf \
    --path-output-vcf example.out.vcf