The Exomiser: Annotate and Filter Variants

Question

[psmirin]

Hi

I downloaded the Exomiser (http://www.sanger.ac.uk/resources/databases/exomiser/query/)and tried to use for the first time , and I am running the following command line:

java -Xms5g -Xmx5g -jar /exomiser-cli-4.0.0/exomiser-cli-4.0.0.jar --prioritiser=phenix -v 278.vcf -I AR -E human -f VCF -F 1 --hpo-ids HP:0006349,HP:0001249,HP:0006349

but I keep getting an error :

2014-10-05 15:55:39,270 WARN de.charite.compbio.exomiser.core.filter.FrequencyFilter [main] - chr1:g.13958C>- frequency data has not been set - Frequency filter failed.

Any suggestion ?

Thank you for your help

[Istvan Albert]

do you have allele frequency in your VCF file?

Answer 1

[karl.stamm]

I can't fix Exomiser but I've used another tool for that kind of task. GEMINI has served me well after processing the VCF with VEP.