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?
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?
Code:
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$
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