SVA Community Plug-ins

 

Welcome to SVA's Community Plugin Library. Here, you will find a repository of Community Plugins, which are files and add-ons to our core SVA program that are contributed by our community of users.

We would like to thank the contributors of these plugins, and hope that the users may find these add-ons handy in their research.

For contributing, please contact: Dongliang Ge, d.ge@duke.edu .

For questions, comments, and bug reports, please directly contact the contributors of each plug-in.

1. HGVS format converter

[Contributed by]:
Dr. Germán Gastón Leparc
Busslinger Lab,
Research Institute of Molecular Pathology Vienna. Campus Vienna Biocenter
leparc@imp.ac.at

[Developing language]:

Perl

[Download]:

HGVS format converter

[Description]:

The script will take as input either an SNV or an INDEL SubjectDetails .csv file. Then depending on the annotation type, it will add extra columns: location, genomic_HGVS, cDNA_HGVS, prot_HGVS "location" is in UCSC format to make it easy to pass on to genome browsers.

Usage would be like this: sva_add_hgvs.pl svainput.SubjectDetails.SNV.csv > sva.hgvsoutput.csv

Below is a list of mutation types that are converted to HGVS format. The HGVS standards are taken from http://www.hgvs.org/mutnomen/

#NON_SYNONYMOUS_CODING aka "missense change" , e.g. p.T26C amino acid Tryptophan-26 changed to a Cysteine
#SYNONYMOUS_CODING aka "synonymous change" , e.g. p.= the protein has not been experimentally analyzed, but no change is expected
#CODING_DISRUPTED_FRAMESHIFT aka "frame shifts" , e.g. p.R97fs there is a frameshift detected - short description is given (no support for fsX# yet)
#CODING_DISRUPTED_OTHER aka "unknown effect" ? , e.g. p.? protein has not been analysed, and effect is expected but difficult to predict
#STOP_GAINED aka "nonsense change" , e.g. p.T26X amino acid Tryptophan-26 changed to a stop codon
#STOP_LOST aka "no-stop change" , e.g. p.X110Q stop codon at position 110 changed to a Glutamine (no support for extX# yet)

Mutations types that are not converted are given blank "-" entries instead of HGVS formatted entries

Here are the mutation types not currently converted:
#UPSTREAM
#DOWNSTREAM
#INTERGENIC
#INTRONIC
#INTRONIC_EXON_BOUNDARY
#ESSENTIAL_SPLICE_SITE
#3PRIME_UTR
#5PRIME_UTR
#EXONIC_NON_CODING_RNA