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
Exome sequencing and targeted capture sequencing
In the SVA annotation and analysis. one has an option to only include genomic regions that are targeted by an exome sequencing or by a targeted capture sequencing.
(1) To use this option, you first need to prepare a text input file like this :
This file has three columns: [chromosome] [start_captured_region] [end_of_the_region]. These columns can be separated by either space or tab.
In most cases, this file is directly available from the manufacturer who provides the exome or targeted capture sequencing assay.
For this purpose, SVA also accepts [chromosome] column in format chr1 or CHR1.
Save this file to a file, say /DIR1/DIR2/DIR3/MyCaptured.txt.
(2) Add this line to your .gsap project file:
Please include the full canonical path (starting with a '/' ) of the file.
Please note this option will include only the variants located within the genomic regions specified in this file in the following annotation and analysis procedures.
© 2011 Dongliang Ge, PhD.