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
Using SVA Analysis functions - Variant Prioritization
The "Variant Prioritization" function is similar to "Gene Prioritization", however it prioritizes specific individual variants instead of entire genes. The variant types are limited to: stop gain, stop lost, and non-synonymous SNPs. This means that this function produces a list of coding variants that responsible for 'knocking out' genes in case genomes. This analysis prioritizes variants by the number of cases containing homozygous genetic variants, absent in control genomes. This analysis tries to answer this simple question: do you see enrichment of protein-truncating or non-synonymous variants in the cases, when compared to control genomes?
Your SVA project must contain at least one case and one control for this function to work. Your SVA project must contain at least two cases for this function to reliably prioritize knocked out genes.
To access the variant prioritization function, go to the menu 'Analysis ->Variant Prioritization'. The Genome Browser must be initilized to run this function.
This will open a 'Prioritization analysis' window. This window will allow you to customize this function in four different ways, explained below. The 'Prioritization analysis' window looks like this:
Function of genetic variantThis section allows you to select the types of 'knock out' variants you wish to include. The three options are:
Criteria for homozygous variants
This section allows you to adjust the coverage you want to require for a homozygous variant. This will impact the number of variants that show up on your gene prioritization output. If you do not care about coverage (i.e. confidence) of the homozygous variants, you can uncheck 'Minimum coverage for a homozygous variant'. Otherwise the default parameters are set as follows:
A brief explanation of default parameters for homozygous variants:
Genetic modelThis section allows you to select the genotype of the variant (heterozygous or homozygous) that you will allow to be present in your control genomes. The target variations in your cases are unaffected by this setting (still homozygous knock out variants).
After selecting your desired settings in the 'Prioritization analysis' window, click 'Output to . . . ' select the file you wish to save your file to, name your file by entering a name into the 'File Name' field and select 'Save'.
After clicking "Save", the path to this file will be displayed in the 'Prioritization analysis' window, then select 'Analyze'.
Sample output (.txt file):
© 2011 Dongliang Ge, PhD.