Installation

Using this software

0. For impatient users
1. Data inputs
- Coordinate system
2. Create a project
3. Annotate a project
- Functional categories
- Using user annotation track
4. Filter for quality scores
5. Main user interface
6. SVA genome browser
- Sections overview
- Identified variants
- Public data
7. SVA tables
- SNV
- INDEL
- SV
8. Selecting genes or regions
- Gene symbol
- Bio-type
- Bio-pathway or GO
- OMIM disorder
- Genomic region
9. Analysis
- Gene prioritization
- Variant prioritization
- Fisher's exact test
10. Exome or targeted capture sequencing
A command line tool
FAQ
Requests and discussions

Using user annotation track

 

Use [USERTRACK] option to include user annotation track

You may want to include user annotation tracks in GFF3 or BED format to perform annotations in addition to the core annotation. To do this, include the following statements:

[USERTRACK]= [YOUR TRACK NAME] , [YOUR TRACK FILE PATH].gff3

[USERTRACK]= [YOUR TRACK NAME] , [YOUR TRACK FILE PATH].bed

 

Multiple user tracks can be included in an SVA .gsap script file.

 

GFF3 format can be used to conveniently store the gene annotation data. Here is an example. The definiton of the GFF3 format can be found here:

http://www.sequenceontology.org/gff3.shtml

 

BED format can be used to conveniently store region-based annotation data, for example, predicted transcription factor binding site data. Here is an example. The definition of the BED format can be found here:

http://genome.ucsc.edu/FAQ/FAQformat.html

 

If your gene annotation files are in GTF format, they can be conveniently converted into GFF3 format using this online tool:

http://www.sequenceontology.org/cgi-bin/converter.cgi

 

 
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