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I am currently using snpEff to do effect prediction and I had a few questions. First, does someone have detailed information about the provenance of the data that was used to create the databases? I.e., where did he get the data to create all of those databases? I can't seem to find that on the website, and in the paper he mentions Ensembl, UCSC, etc. but no details.
I am also trying to create a new database for snpEff using another annotation, and I am running into problems. The annotation is a xenoRefGene annotation from UCSC, which means that it is genes from other organisms mapped to our genome of interest. However, this means that some of the genes/gene families might be mapped to more than one location. This seems to be causing problems in building the database, because I get many errors that look like this when I run snpEfff build:
Ignoring exon outside chromosome range (chromo length: 80642250). Exon: 6:82316946-82317137 'exon_chr7_82316947_82317138' rank:0, sequence:
It looks like the exon it is seeing is from the same gene, but a different chromosome. I looked at the gene IDs and they are the same for those two regions. Does anybody know of any scripts, or are there options in snpEff to deal with this sort of issue? Any help would be highly appreciated. Thanks!
- Nik.
I am also trying to create a new database for snpEff using another annotation, and I am running into problems. The annotation is a xenoRefGene annotation from UCSC, which means that it is genes from other organisms mapped to our genome of interest. However, this means that some of the genes/gene families might be mapped to more than one location. This seems to be causing problems in building the database, because I get many errors that look like this when I run snpEfff build:
Ignoring exon outside chromosome range (chromo length: 80642250). Exon: 6:82316946-82317137 'exon_chr7_82316947_82317138' rank:0, sequence:
It looks like the exon it is seeing is from the same gene, but a different chromosome. I looked at the gene IDs and they are the same for those two regions. Does anybody know of any scripts, or are there options in snpEff to deal with this sort of issue? Any help would be highly appreciated. Thanks!
- Nik.