snpEff for bacteria genome

Question

[maricom]

Hi all,

I'm trying to annotate bacteria genome using SnpEff. Variants were detected using gatk HaplotypeCaller.

I'm wondering what kind of options do I have to use for bacteria genome?

My current command is like this.

java -jar snpEff.jar -c snpEff.config -i vcf -o vcf database input.vcf > output.vcf

Thank you in advance!

[finswimmer]

Hello,

what's the name of your bacteria? How does your snpEff.config looks like? Is database just a placeholder here?

fin swimmer

[maricom]

Hi,

Thank you for your reply.

I obtained this genome, so I created db.

GTF file is like this.

seqname     source   feature start end   score strand frame attribute
bacteria1   bacteria1   CDS 101     1507    .   +   0   gene id "bacteria1_0001";
bacteria1   bacteria1   CDS 1569    2666    .   +   0   gene id "bacteria1_0002";
bacteria1   bacteria1   CDS 2663    4378    .   +   0   gene id "bacteria1_0003";

snpEff.config is like this.

bacteria1.genome :bacteria1
bacteria1.bacteria1.codonTable : Bacterial_and_Plant_Plastid