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

Using SVA Analysis functions - Fisher's exact test

 

SVA implements the Fisher's exact test as one way to examine the association between genetic variants and the target trait or disease of interest.

Requirement of this test

This function requires the case/control status is specified in the pedinf file, which is an optional input file for an SVA project. This file can be specified using this statement in the SVA project file: '[PEDINFO]='. Here is the description and example of of this file.

This function also assumes that the studied subjects are not biologically related, i.e., although the pedinf file itself is in a linkage format, no members from the same family should be included in this test.

Performing this test

To access the Fisher's exact test function, go to the menu “Analysis ->Fisher's exact test '.

Then you will be asked to specify the output file. Five genetic models will be tested:

Allelic
Trend
Genotypic
Dominant
Recessive

The results for each model will be outputted to a separate file. For example, if you specify the output file as 'MyFisherTest', the output files will be:

MyFisherTest.allelic.out
MyFisherTest.trend.out
MyFisherTest.geno.out
MyFisherTest.dom.out
MyFisherTest.rec.out

There are 7 columns in the output file:

Column Name Description
1 ID Variant ID
2 CHR Chromosome
3 Allele1 Allele 1 of the variant
4 Allele2 Allele 2 of the variant
5 Geno_Case Genotype count in cases
6 Geno_Ctrl Genotype count in controls
7 P P value under the genetic model specified in the file name

Each result file is ordered by column 7, the P value, in an ascending order. Here is an example of the output file:

ID CHR Allele1 Allele2 Geno_Case Geno_Ctrl P
X_12623441_A X 1 2 7/0/3 0/3/7 0.002392

How this test is performed

SVA prepares the variant data in linkage formats and uses an independent software tool, , to perform the Fisher's exact test. PLINK is a software tool authored by Shaun Purcell at the Center for Human Genetic Research , Massachusetts General Hospital, and the Broad Institute of Harvard & MIT. SVA user does not need to download and install PLINK separately.

 
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