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scores's Introduction

Scores

Description of scores used for genomic interpretation of variants.

List of scores:

Format:

  • Name
  • Version
  • Type = {Score | Metascore}
  • Category = {Conservation | Functionnal}
  • Usefull for = {to define}
  • Short description
  • Orientation and range
  • Methodology
  • VCF description (VEP)
  • Long Description
  • Exemple
  • Source

As some score are based on other scores the following array should ive a nice overview of their interactions:

Metascores/scores Number of annotations GERP phastCons phyloP Grantham SIFT PolyPhen MutationTaster MutationAssessor FATHMM LRT SiPhy 1000G AF ESP AF ClinVar HGMD gnomAD/BRAVO variant density VEST PROVEAN MutPred Gene Annotation? bstatistic mirSVR targetScan chromHMM Encode expresion Encode nucleosome position Encode histone modification Encode open chromatine Encode DNAse hypersensitiv Encode promoter-associated regulatory features JASPAR Segway tOverlapMotifs TFBS mutationDensity nearestMutation dbscSNV GC CpG NNSplice CADD MetaLR/SVM multiple-sequence alignment RVIS24 PAM250 BLOSUME62 BioPlex 2.0 Network CORUM PrePPI dbPTM GPS-SUMO GPS3.0 UbiProber Exac (pLI, pRec, lof_z) domino s_het Eigen missense baldness
DANN 63 X X X X X X X X X X X X X X X X X X X X X X X X X X
CADD 63 X X X X X X X X X X X X X X X X X X X X X X X X X X
MetaLR/SVM 10 X X X X X X X X X X
REVEL 13 X X X X X X X X X X X X X
MutationTaster2 X X X X X X X X X X
VEST 2 X X
M-CAP 413 X X X X X X X X X X X X 397 X X X
MVP X X X X X X X X X X X X X X X X X X X X X X X X X X X X
MPC 4 X X X X

An array resume of Performance evaluation of pathogenicity-computation methods for missense variants

Tools resume

<> Source S10

<>Source S10

Some scores are more or less correlated as we can see on :

  • the Meta publication dataset :

Meta sores correlation plot

  • the Eigen publication dataset :

Eigen scores correlation plot

  • the MVP publication dataset :

MVP scores correlation plot

Another tool correlation

scores's People

Contributors

mlebeur avatar

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