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
This page will describe the structure and function of the table listing SVs.
Since the methods for calling structural variation using next-generation sequencing techniques are quickly evolving, the structure and function of this table are subject to significant changes too.
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. A "confidence score filter" allows one to perform quality score filter on SVs. This process is detailed here.
B.2. An "SV type filter" allows one to select SVs based on the type of the SVs.
B.3. An "calling method filter" allows one to select SVs based on the calling method.
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.
As in the current version, the displayed columns are:
SV ID, SV serial number, number of subjects carrying SV, chromosome, type of SV, start, end, size of SV, number of reads (for read pair method), ambiguous start, ambiguous end, if overlapping with a DGV record, overlapping DGV record ID, the percentage of SV overlapping with DGV record, the percentage of DGV record overlapping with SV, function, transcript, KEGG pathway, gene ontology term, calling method, if present in control genomes.
E. Hyperlinks (in blue) are clickable for details. In the SV table, three items are hyperlink-enabled:
G.1 SV ID. Clicking on this item will browse this SV in SVA genome browser.
G.2 Number of subjects carrying SV. Clicking on this item will show the subject details.
G.3. Transcripts. Clicking on this item will browse this transcript in SVA genome browser.
© 2011 Dongliang Ge, PhD.