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Annotations

Scout is a primarily a visualisation tool with some other functionality. One could imagine that in the future, some or all annotations could be performed by Scout. For now scout will look for some known keys when uploading a VCF and extract information for those. VEP is the tool supported for functional and regional annotations at the moment, SnpEff will be added in the near future. For the other types of annotations Scout will look for certain keys in the INFO field of the vcf and expect the value to be of a specific type. This means that there is not a dependency on any other specific annotation tool besides VEP, just make sure that the key and values are correct according to the specification below.

Rank score

One of the hard problem when dealing with whole genome data is the huge amount variants that are generated in every analysis. Scout was developed to be used in rare variant analysis, this means that there is ony a small number of variants that are actually interesting to look at. We do not want to store all variants from each case in a database that should be able to controll thousands of cases. To solve this problem we are working with rank scores, each variant is scored according to a scoring schema then we only upload and sort the variants based on their rank score. In this way the users can start by looking at the variants that looks potentially most dangerous from a bioinformatic perspective. We use the tool genmod to (among other things) score the variant, but as long as there is a RankScore-field in the INFO field of the VCF with a float as value it is handeled by Scout.

Annotation keys and tool suggestions

In this section all the different annotation keys and suggestions of tools that can be used to annotate them are listed.

Frequencies

1000G

The frequency from the 1000G population database.

1000G_MAX_AF

The maximum allele frequency of all populations in the 1000G population database.

  • Key: 1000G_MAX_AF
  • Value: Float
  • Tools: custom made, we have modified the 1000G file and use genmod

ExAC

The frequency from the ExAC population database.

ExAC_MAX_AF

The maximum allele frequency of all populations ExAC population database.

  • Key: EXAC_MAX_AF
  • Value: Float
  • Tools: custom made, we have modified the exac file and use genmod

Severity

CADD score

The Combined Annotation Dependent Depletion(CADD) score. A prediction of the deleterioussness for a variant.

SIFT

The SIFT) prediction for how a variation affects the protein.

  • Key: CSQ-SIFT
  • Value: String
  • Tools: VEP

PolyPhen

The PolyPhen) prediction for how a variation affects the protein.

  • Key: CSQ-PolyPhen
  • Value: String
  • Tools: VEP

Rank score

The combined rank score for a variant

  • Key: RankScore
  • Value: Float
  • Tools: genmod

Conservation

Gerp

The Genomic Evolutionary Rate Profiling(GERP) conservation string. An estimation of how conserved this position is.

  • Key: GERP++_RS_prediction_term
  • Value: String
  • Tools: SnpSift

phastCons

The PHASTcons conservation string.

  • Key: phastCons100way_vertebrate_prediction_term
  • Value: String
  • Tools: SnpSift

phylop

The phylop 100 way predicted conservation string.

  • Key: phyloP100way_vertebrate_prediction_term
  • Value: String
  • Tools: SnpSift

Inheritance

Genetic models

What genetics models are followed for the variant in the particular family

  • Key: GeneticModels
  • Value: list of String
  • Tools: genmod

Autosomal Recessive Compounds

What variants is this variant in Autosomal Recessive Compound with?

  • Key: Compounds
  • Value: list of String
  • Tools: genmod