SpliceSiteVariantAnalyzer (SSVA)
I. Introduction
II. Installation Instructions
III. Usage Instructions and Examples
IV. Contact
SpliceSiteVariantAnalyzer (SSVA) is a splice site variant diagnosis tool which outputs a comprehensive annotation for splice site variants from a vcf file. The software is compatible with both hg19 or hg38 as the reference.
This output includes the following:
To install SSVA locally follow these steps:
mvn clean -U install
java -jar target/SSVA-1.0-jar-with-dependencies.jar -help
to see command line optionsRequired Databases: SSVA uses different databases and software to provide its results. Below are instructions on how to download and install the required databases and software.
The main package download for Annovar can be found here. Once Annovar software has been downloaded, it can be used to download other required databases. To download the additional databases use the following command for each database:
./annotate_variation.pl -buildver hg19 -downdb -webfrom annovar <name of db> <output_folder(usually humandb/)>
The abbreviations for the databases (\<name of db>) used by SSVA are as follows:
SSVA requires either the hg19 or hg38 genome separated by chromosome. Instructions on how to download this are given on UCSC website here. The files must be uncompressed as explained in the previous link.
Both the hg38 and hg19 RefSeq files are included in the main directory of the github repository, therefore the user does not need to download their own RefSeq file. These files comes from the UCSC table browser.
The MaxEntScan scripts are already downloaded in the git repository under the MES
and splicemodels
directories, therefore the user does not need to download the MES scripts. These scripts were downloaded from https://github.com/razZ0r/maxentscan.git.
Required command line arguments:
Optional command line arguments:
An example for running the program is as follows:
java -jar ./target/SSVA-1.0-jar-with-dependencies.jar \
-i chromosome22.vcf \
-o SVA_output/ \
-a ~/software/annovar \
-d ~/humandb/ \
-g ~/hg19Ref/ \
For questions, comments, concerns, feature requests, suggestions, etc., please contact:
Pery Ridge, Ph.D. -- perry.ridge@byu.edu
Note: For usage questions, please consult section `III. Usage Instructions and Examples' first.