Variant Annotation Tutorial

Step 1: Create a Directory

Run the following command to create a directory for your work:

mkdir Mydirectory

Step 2: Download snpEff

You can download snpEff from its official website: snpEff Download

Step 3: Unzip snpEff

Unzip the downloaded snpEff files.

Step 4: Check Pre-Built Databases

To list pre-built databases in snpEff, run the following command:

java -jar snpEff.jar databases

Step 5: Download GFF and Fasta Files

Download the required files for Gossypium hirsutum:

• Genome FASTA File
• Annotation GFF3 File

Step 6: Unzip Files

Unzip the downloaded files using the following command:

gzip -d filename.gz

Step 7: Organize Files

Create a directory and move the files:

mkdir data/hirsutum
mv genome.Ghir.CRI.fa data/hirsutum/sequences.fa
mv gene.Ghir.CRI.gff3 data/hirsutum/genes.gff

Step 8: Edit Configuration File

Edit the snpEff.config file to add the following line at the end:

hirsutum.genome : Gossypium hirsutum

You can use a text editor like vi:

vi snpEff.config

Step 9: Build the Database

Run the following command to build the database:

java -jar snpEff.jar build -gff3 -v hirsutum

Step 10: Annotate Variants

To annotate variants from a VCF file, use this command:

java -jar snpEff.jar ann hirsutum filename.vcf > out.ann.vcf

References

For more details, visit the official snpEff guide: snpEff Documentation

Reference: "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3." Cingolani P, et al. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672.