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NAME

Sanger::CGP::Vagrent::Bookmarkers::MostDeleteriousBookmarker - Finds the AnnotationGroup with the most severe consequence from the supplied list

DESCRIPTION

This bookmarker will mark/return the Sanger::CGP::Vagrent::Data::AnnotationGroup with the most catastrophic consequence from the list of supplied groups.

It inherits from Sanger::CGP::Vagrent::Bookmarkers::AbstractBookmarker and Sanger::CGP::Vagrent::Bookmarkers::RepresentativeTranscriptBookmarker

When handed an array of Sanger::CGP::Vagrent::Data::AnnotationGroup objects it will sort them into the same order as the RepresentativeTranscriptBookmarker does and then prioritise AnnotationGroups by matching their ontology terms to the following hierarchy. The highest priority AnnotationGroup is considered to be the match

1 Complete protein loss
2 Frameshift
3 Stop gained/Nonsense
4 Essential splice site change in CDS
5 In-frame codon loss
6 Simultaneous in-frame codon loss and gain
7 In-frame codon gain
8 Initiator/start codon change
9 Terminator/stop codon change
10 Non-synonymous/Missense
11 Complex change in CDS
12 Complete non-coding transcript loss
13 Synonymous/Silent
14 Premature start codon gained in 5'UTR
15 Essential splice site change in 5'UTR
16 Essential splice site change in 3'UTR
17 Essential splice site change in non-coding transcript
18 Exonic change in 3'UTR
19 Exonic change in 5'UTR
20 Splice region change in CDS
21 Splice region change in 5'UTR
22 Splice region change in 3'UTR
23 Splice region change in non-coding transcript
24 Complex change in mRNA
25 Change in non-coding transcript
26 Intronic change
27 Upstream change
28 Downstream change

NOTE

The rank in the hierarchy is calculated for each Sanger::CGP::Vagrent::Data::AnnotationGroup in isolation, and comparison between AnnotationGroups is based solely on the ranks. There is no consideration given to variants that are annotated to multiple genes and only the Sanger::CGP::Vagrent::Data::AnnotationGroup with the most disruptive effect will be returned.

METHODS

see Sanger::CGP::Vagrent::Bookmarkers::AbstractBookmarker

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