How to Use snpeff to analyze SNP results

Snpeff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on Genes

For more information, see:

Http://snpeff.sourceforge.net/SnpEff_manual.html

 

1. installation:

First, download the installation package in the home directory.

Wget http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip

Decompress the package

Unzip snpeff_latest_core.zip

All programs in the snpeff directory will be generated.

2. Configure your own genome and annotation files. The official database contains a large number of reference genome files, which generally do not need to be configured. If it is not found in the official database, you need to configure it yourself

Assume that I have a reference genome: osativa_204.fa

There is a comment file for this genome: osativa_204_gene.gff3

First, edit the configuration file and add the entry to the new genome.

The configuration file is in the snpeff directory and the configuration file name is snpeff. config

Use VI to edit and add the following two lines

# Rice genome, version osativa_204
Osativa_204.genome: Rice

Save and exit

Or in the snpeff file, create the directory data

Mkdir data

CD Data

Create the osativa_204 and genomes Directories

Mkdir osativa_204

Mkdir genoems

Put your gff3 comment file in the osativa_204 directory

Put your reference sequence file under the genomes directory

Note: Rename the annotation file genes. gff.

Return to the snpeff directory and run the following command:

Java-jar snpeff. Jar build-gff3-V osativa_204

 

Run:

Copy the VCF file to the data directory first.

Then run the following command in the snpeff directory:

Java-xmx8g-jar snpeff. Jar osativa_204 data/testgroup. Filtered. Ordered. VCF> test. Eff. VCF

After the command is executed, three files are generated in the snpeff directory.

Snpeff_genes.txt

Snpeff_summary.html

Test. Eff. VCF

Then, open snpeff_summary.html in the browser to view the summary of the results.

 

 

 

 

By freemao

Fafu.

[Email protected]

 

How to Use snpeff to analyze SNP results