The Exomiser: Annotate and Filter Variants
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
1 answer
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.
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do you have allele frequency in your VCF file?