Using this software0. For impatient users
1. Data inputs
2. Create a project
3. Annotate a project
Using user annotation track
4. Filter for quality scores
5. Main user interface
6. SVA genome browser
7. SVA tables
8. Selecting genes or regions
Bio-pathway or GO
Fisher's exact test
10. Exome or targeted capture sequencing
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, firstname.lastname@example.org .
For questions, comments, and bug reports, please directly contact the contributors of each plug-in.
1. HGVS format converter
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
Mutations types that are not converted are given blank "-" entries instead of HGVS formatted entries
Here are the mutation types not currently converted:
© 2011 Dongliang Ge, PhD.