jvlasblom
commented
10 years ago Closing this issue as mostly irrelevant, as MedSavant now at least stores all types of variants. While importing variants, it's still possible for MedSavant to maintain a list of 'skipped' variants that it won't feed to Jannovar, which might improve Jannovar performance. I think it's unlikely that performance will be affected much though, as Jannovar should skip over unrecognized variants anyway with minimal overhead.
Consider calling Jannovar after prefiltering variants. MedSavant may not know how to deal with certain kinds of VCF input lines, and there's no point trying to annotate these with Jannovar. MedSavant could prefilter these out and give cleaner input to Jannovar, possibly also speeding up Jannovar annotation.