I am trying to annotate my vcf file (my.vcf.gz) with gnomad using SnpEff/SnpSift. I downloaded gnomad (3.1.1) as given in the instructions GNOMAD download
I now want to annotate my vcf.gz file, containing variants from all chromosomes, with this data. The SnpSift example page SnpSift gives the example:
java -jar SnpSift.jar annotate dbSnp132.vcf variants.vcf > variants_annotated.vcf
However, the vcf file downloaded from gnomad is not a single file, but one file for each chromosome. For example:
gnomad.genomes.v3.1.1.sites.chr10.vcf.bgz.tbi gnomad.genomes.v3.1.1.sites.chr19.vcf.bgz.tbi gnomad.genomes.v3.1.1.sites.chr5.vcf.bgz.tbi
What command do I need so that it uses all the vcfs in the downloaded gnomad directory?
Thanks for your help!