How to get snpEff working with bacterial genomes from NCBI
16 Nov 2012You can do this from GFF files. You need the GFF file and corresponding FNA file.
Create a nickname
<databasename>
and add to “genomes” list at top of snpEff.config.
Add a line at the bottom of snpEff.config:
<databasename>.genome : Descriptive Name
The FNA should be renamed and the header line rewritten to match the GFF header:
data/genomes/<databasename>.fa
The GFF file should go in:
data/<databasename>/genes.gff
Then build the database:
java -jar bin/snpEff_2_0_5d/snpEff.jar build -gff3 -v <databasename>
Ensure the snpEff.config has the bacterial codon table selected:
<databasename>.genome : <description>
<databasename>.chromosomes : <fastahdrid>
<databasename>.<fastahdrid>.: Bacterial_and_Plant_Plastid
The VCF file also needs to match the modified header
Then:
java -jar bin/snpEff_2_0_5d/snpEff.jar eff -no-downstream -no-upstream -no-utr -no-intergenic -o vcf -c snpEff.config <databasename> vcffile