Snpeff / Annovar with Cricetulus griseus

[nasepu]

I'm trying to annotate a batch of SNPs from chok1 cells. Unfortunately, the database for them isn't included with either snpeff or annular. I have reference sequence, and gene files in gff, fasta, and genbank format from chogenome.org.

Sadly, whenever I try to create a new database in snpeff I get "file not found" errors, as seen below. (with ls at the end to show that the program is clearly a filthy liar).

Annovar requires a refgene file which I've never heard of before, and can't find a way to convert anything to.

Any ideas / other annotators that might work with nonstandard organisms?

dhcp-128-32-88-64:snpeff BIOINFORMATICS$ java -Xmx4g -jar snpEff.jar build -gff3 -v cho
00:00:00.000	Building database for 'cho'
Reading GFF3 data file  : '/Users/BIOINFORMATICS//snpEff/data/cho/genes.gff'
	Reading genes       : java.lang.RuntimeException: File not found '/Users/BIOINFORMATICS//snpEff/data/cho/genes.gff'
	at ca.mcgill.mcb.pcingola.util.Gpr.reader(Gpr.java:466)
	at ca.mcgill.mcb.pcingola.util.Gpr.reader(Gpr.java:437)
	at ca.mcgill.mcb.pcingola.snpEffect.factory.SnpEffPredictorFactoryGff.readGff(SnpEffPredictorFactoryGff.java:219)
	at ca.mcgill.mcb.pcingola.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:96)
	at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdBuild.createSnpEffPredictor(SnpEffCmdBuild.java:96)
	at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:240)
	at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:257)
	at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:75)
java.lang.RuntimeException: Error reading file '/Users/BIOINFORMATICS//snpEff/data/cho/genes.gff'
java.lang.RuntimeException: File not found '/Users/BIOINFORMATICS//snpEff/data/cho/genes.gff'
	at ca.mcgill.mcb.pcingola.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:134)
	at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdBuild.createSnpEffPredictor(SnpEffCmdBuild.java:96)
	at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:240)
	at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:257)
	at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:75)
00:00:00.167	Finishing up
dhcp-128-32-88-64:snpeff BIOINFORMATICS$ cd data
dhcp-128-32-88-64:data BIOINFORMATICS$ cd cho
dhcp-128-32-88-64:cho BIOINFORMATICS$ ls
genes.gb	genes.gff	genes.txt	sequences.fa
dhcp-128-32-88-64:cho BIOINFORMATICS$ pwd
/Users/BIOINFORMATICS/snpeff/data/cho
dhcp-128-32-88-64:cho BIOINFORMATICS$

[Gig77]

CooVar does not depend on external databases and works directly from GFF files.

http://www.biomedcentral.com/1756-0500/5/615/abstract