dbNSFP mutation scores¶
Introduction¶
The dbNSFP database curates a large collection of mutation scores that can reveal very useful for variant effect analysis, including benchmarking of new variant effect tools.
How to fetch mutation scores from the dbNSFP database¶
We can retrieve mutation scores for a given set of input mutations using the command line from the ENSEMBL-VEP alongside the dbNSFP 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 dbNSFP,/workspace/datasets/vep/homo_sapiens/plugins/dbNSFP4.5a_grch38.gz,\
SIFT_score,SIFT4G_score,Polyphen2_HDIV_score,Polyphen2_HVAR_score,MutationAssessor_score,FATHMM_score,MetaLR_score,MetaRNN_score,CADD_raw,VEST4_score,PROVEAN_score,REVEL_score,ESM1b_score,EVE_score,AlphaMissense_score,phyloP100way_vertebrate,phyloP470way_mammalian,phyloP17way_primate
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.
Right after --plugin dbNSFP,/workspace/datasets/vep/homo_sapiens/plugins/dbNSFP4.5a_grch38.gz and separated by commas it goes the list of all the accepted scores that you want to be mapped to your query mutations. You can check out the full list of scores here:
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