MaveDB mutation scores¶
Introduction¶
The MaveDB is a public repository for datasets from Multiplexed Assays of Variant Effect (MAVEs), such as those generated by deep mutational scanning (DMS) or massively parallel reporter assay (MPRA) experiments.
How to fetch mutation scores from the MaveDB database¶
We can retrieve mutation scores for a given set of input mutations using the command line from the ENSEMBL-VEP alongside the MaveDB plugin.
Within an interactive session in the cluster, you can use the following command line as a template and modify it according to your specific needs:
singularity exec /workspace/datasets/vep/homo_sapiens/ensembl-vep_111.0.sif vep --dir /workspace/datasets/vep/ \
--tab -i input_mutations.tsv --offline --cache -o output_annotated_mutations.tsv \
--species homo_sapiens --assembly GRCh38 --fork 8 --canonical \
--plugin MaveDB,file=/workspace/datasets/vep/homo_sapiens/plugins/MaveDB_variants.tsv.gz
Remarks¶
input_mutations.tsv must be in an accepted format for VEP, a tab separated file with chromosome, start, end and variant like in the following example will work.
output_annotated_mutations.tsv is the filename of the output.
--canonical is a VEP command line option, it simply adds a column pointing out whether the transcript is canonical.
Bear in mind that some scores have several tracks of data and some postprocessing might be required after the query.
Reference¶
Ferran Muiños, Paula Gomis, Miguel Grau
Updated 2024/07/01