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

SVA tables

 

The SVA tables separately list annotated single nucleotide variants (SNVs), INDELs, and structural variants (SVs). These tables also respond to different filters that the users may apply.

These lists are firstly ordered by chromosome, and then by the locations of the variants.

The structures and behaviors of these three tables are similar:

  • A. A drop down box allows a user to select a functional category.
  • B. There are a number of other filters also available for selecting variants.
  • C. By default one table page can display up to 1000 records. A drop down box allows a user to select different pages based on genomic locations.
  • D. Exporting the variant list to a text file, including the full-length list but not only the records listed on this page.
  • E. Blue hyperlinks are always clickable for details.

 

 
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© 2011