I am annotating variants for clinical diagnosis. One of the data required by my team is REVEL. We work with specific transcripts so when clinicians do variant interpretation, they need to check if our preferred transcript is among the transcripts considered.
REVEL is not a transcripts-specific pathogenic prediction tool but since the last release (2021) revel provided the transcripts considered for each genetic position. For example:
chr hg19_pos grch38_pos ref alt aaref aaalt REVEL Ensembl_transcriptid
1 2700309 2783764 T C S G 0.163 ENST00000401094;ENST00000401095
So as this was developed by the previous bioinformatician, this is pointless because the score is given in the vcf files. However, clinicians need to open the REVEL table for each variant to be analysed and check if our transcript ID is or not considered by REVEL.
What I want is to do is to add the transcripts ID next to the score so clinicians don't need to do the manual checking. Can I do this by changing some of the VEP parameters.
So far my code is this
# TODO: Add the VEP module, update the plugin and cache paths
logmessage "INFO: Annotating with VEP & REVEL..."
vep \
--cache \
--dir_cache "$vepcache" \
--dir_plugins "$vepcache"/Plugins \
--species homo_sapiens \
--merged \
--assembly "$genomeversion" \
--format vcf \
--vcf \
--force_overwrite \
--plugin REVEL,"$vepcache"/Plugins/new_tabbed_revel.tsv.gz \
--use_given_ref \
--no_stats \
--fork 4 \
--offline \
--fasta "$refgenome" \
--exclude_predicted \
--input_file "$RunID".SNPEff.vcf \
--output_file TEMP."$RunID".REVEL.vcf
More info I can add to clarify this issue.
The reason of this question is because, although REVEL scoring is genomics base and not a transcripts base pathogenic metric (as I understand) there are some position with more than one score, to be more exact the 3.66% (3,999,580 of 82,100,678) of the bases have >1 score.