i have a proble running the tool: it says it does not find the annotation data, but i’m 100% sure that the annotation was properly extracted from the .zip file into the same directory as VcfAnnot
$ groovy VcfAnnot.groovy ./genotype.raw.vcf
Pre-loading RefGene data
Caught: java.io.FileNotFoundException: null/refseq_coords.txt (No such file or directory)
java.io.FileNotFoundException: null/refseq_coords.txt (No such file or directory)
at variant.VcfAnnot.run(VcfAnnot.groovy:242)
ls shows, that the refseq_coords.txt file is present in the directory.
very kind you’ve responded so quickely, yet there seems to be another problem: when you click on the script download link, this error message appears: “AccessDeniedAccess DeniedB929932C31092578MiYMWLwiFj3TlrWXoIIOpcNQQV0wfECyYB6QU8f34xVZHfJ9GEocbwgIOagrI2m2”
100bp 
i have a proble running the tool: it says it does not find the annotation data, but i’m 100% sure that the annotation was properly extracted from the .zip file into the same directory as VcfAnnot
$ groovy VcfAnnot.groovy ./genotype.raw.vcf
Pre-loading RefGene data
Caught: java.io.FileNotFoundException: null/refseq_coords.txt (No such file or directory)
java.io.FileNotFoundException: null/refseq_coords.txt (No such file or directory)
at variant.VcfAnnot.run(VcfAnnot.groovy:242)
ls shows, that the refseq_coords.txt file is present in the directory.
What is the problem?
Sorry, corrected. Try downloading the script again, should work for now. Or try “VcfAnnot.groovy ./genotype.raw.vcf .”
hey,
very kind you’ve responded so quickely, yet there seems to be another problem: when you click on the script download link, this error message appears: “AccessDeniedAccess DeniedB929932C31092578MiYMWLwiFj3TlrWXoIIOpcNQQV0wfECyYB6QU8f34xVZHfJ9GEocbwgIOagrI2m2”
Should be working by now