I am trying to run snpEff to functionally annotate mutations identified in a GWAS, with coordinates based on the hg19 genome.

I uploaded and installed the hg19 reference genome as

  java -jar snpEff.jar download hg19

so that now there is a /data/hg19/ directory in the snpEff folder containing sequence.bin files.

When I attempt to run snpEff

java -jar npEff.jar /<nydir>/snpEff/data/hg19 ./chr22.dose.vcf > chr22_annotated.vcf

I get an error stating that hg19.genome is not found in the snpEff.config file. I'm not sure what I need to add to the config file in order to get this to work.

There already is a line in the config file

hg19.genome: Homo_sapiens (UCSC)
hg19.reference: http://ghdownload.cse.uscc.edu \

etc. So it seems like my choices are either to edit the config file to have it recognize my internal reference directory, or else modify my snpEff script to leverage the links listed in the config file for the h19 genome.

If someone with experience using snpEff could provide information on how to do one or the other (or both), it would be very helpful.