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SACGF / variantgrid

VariantGrid public repo
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Put back raw pathogenicity scores for ACMGv4 #1130

Open davmlaw opened 3 months ago

davmlaw commented 3 months ago

We moved to rankscore, but raw scores are used in ACMGv4 in PP3_supporting

Check out if any others are used

We should also run eg REVEL as a tool instead of dbNSFP

If not on the short variants then def on SVs as can't look them up

davmlaw commented 2 months ago

There are new plugins in VEP 112, some probably already available in dbnsfp and examine other ones not in there:

Enformer - adds pre-calculated predictions of variant impact on gene expression BayesDel - adds a deleteriousness meta-score combining multiple deleteriousness predictors OpenTargets - adds locus-to-gene (L2G) scores to predict causal genes at GWAS loci from Open Targets Genetics New plugins (supported on CLI): DeNovo - identifies de novo variants in a VCF file. This plugin requires a pedigree (.ped) file. SpliceVault - predicts exon-skipping events and activated cryptic splice sites based on the most common mis-splicing events around a splice site DosageSensitivity - annotates the likelihood of a gene being haploinsufficient or triplosensitive VARITY - adds pre-calculated pathogenicity scores of rare human missense variants