Several questions I'm hoping you guys can help me resolve:
1) Does anyone know what build the current release of ClinVar uses for hg19? Is it UCSC hg19, or is it 1000 genomes GRCh37. I know it doesn't matter for autosomes, but I'm trying to import databases to ANNOVAR for mitochondrial variant annotation, and mito contig data is not the same between the builds (or at least it wasn't until UCSC finally updated their hg19 build to the rCRS a few months ago).
2) Does anyone know how to use table_annovar.pl to mix database types for multianno? I ran table_annovar.pl in general as follows (~~~ = pathway placeholder:
perl ~~~/annovar/table_annovar.pl variants.vcf ~~~/annovar/humandb/ --outfile ~~~/variants --buildver GRCh37_MT --protocol ensGene,MMpolymorphisms,MMdisease --operation g,f,f --vcfdbfile ~~~/annovar/humandb/GRCh37_MT_MMpolymorphisms.vcf,~~~/annovar/humandb/GRCh37_MT_MMdisease.vcf --vcfinput
The vcfdbfile argument did not seem to work as intended for my filter databases as I got the following error message:
Error: the required database file ~~~/annovar/humandb/GRCh37_MT_MMpolymorphisms.txt does not exist.
Seems like it wants a generic annovar .txt format database despite my vcfdbfile specification. The vcfdb is in the proper location.
3) Is there a way to easily convert databases into generic annovar database format, apart from manual conversion? I looked into -downdb -webfrom solutions and the program couldn't seem to pull files from any valid html.