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Pathogenicity Scoring
Score and rank variants from an annotated VCF (SnpEff/ANNOVAR). Choose an existing OmniObject or upload a file.
Plugin:
pathogenicity_scoring
Input:
annotated VCF
Output:
ranked variants
All Plugins
Start a run
Select how you want to provide input.
Use OmniObject
Upload annotated VCF
Choose OmniObject
Pick an existing annotated VCF artifact produced by your annotation plugins.
Annotated VCF object
— Select an OmniObject —
Tip: If you don’t see your object here yet, upload the file using the Upload option.
Upload annotated VCF
Supported:
.vcf
,
.vcf.gz
,
.vcf.xz
. SnpEff VCFs with
INFO/EFF
and ANNOVAR-annotated VCFs are accepted.
File
If you upload, the plugin will store it in the run workspace and score from that copy.
Scoring settings
Model
Basic (impact + consequence)
Predictors (CADD/REVEL/SpliceAI) — coming soon
Top N
Require PASS filter
No
Yes
Pick worst transcript by
Impact (HIGH > MODERATE > LOW > MODIFIER)
Effect severity (custom map)
Include MODIFIER variants
Yes
No
Run
Run Pathogenicity Scoring
After submission, you’ll be redirected to the run page where you can monitor status and view results.