Closed Kurt-Hetrick closed 5 years ago
In regards to the final reports (item #1). I think that I'm going to do a downward liftover from 38 to 37 using the vcf file and then used the downward liftover to compare to the final report file.
https://broadinstitute.github.io/picard/command-line-overview.html#LiftoverVcf
just a note to think about the modeled centromeres. possibly flag them in the vcf using heng li's repeat mask track.
so, annovar databases are not for me. waiting on hua/yan for that. the modeled centromeres thing. i'll add them as variables in case I decide to push them out at some time. otherwise everything else in here is done.
marking this as done
this is mostly for things that I don't have direct control over.