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

Table for single nucleotide variants (SNVs)

 

This page will describe the structure and function of the table listing SNVs.

A. A drop down box allows a user to select a functional category, illustrated below. The definition of these functional categories are detailed here.

B. There are a number of other filters also available for selecting variants.

B.1. An "NS filter" allows one to select only "intolerant non-synonymous SNV" defined by MAPP.

B.2. A "homozygosity filter" allows one to select only homozygous (in any subjects) SNVs

.

B.3. A "refSNP filter" allows one to select only reference SNV, or "novel" SNV.

B.4 A "confidence score filter" allows one to perform quality score filter on SNVs. This process is detailed here.

B.5. An "RMR filter" allows one to select SNVs located in a repetitive region, or a non-repetitive region. Repetitive region here is defined using RepeatMasker.

B.6. A "HapMap Freq Filter" allows one to select SNV based on HapMap CEU minor allele frequency , if available. The HapMap allele frequency is limited to CEU population as in the current version.

C. A drop down box allows a user to select different pages based on genomic locations. By default one table page can display up to 1000 records.

D. Exporting the variant list to a text file, including the full-length list but not only the records listed on this page.

E. A "displayed columns" button determine the columns showed in the table (F). Clicking on this table activates this dialog:

F. The table. Its content is determined by button "displayed columns" (E).

G. Hyperlinks (in blue) are clickable for details. In the SNV table, four items are hyperlink-enabled:

G.1 SNV ID. Clicking on this item will browse this SNV in SVA genome browser.

G.2 Number of subjects carrying SNV. Clicking on this item will show the subject details.

G.3. Some functional category, including non-synonymous coding, stop-gained, stop-lost. Clicking on this item will show more details.

G.4. Transcripts. Clicking on this item will browse this transcript in SVA genome browser.

 

 
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