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Kurt-Hetrick / CIDR_WES

CIDR's production pipeline for WES and other targeted DNA sequencing projects.
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things to convert for grch38 #28

Closed Kurt-Hetrick closed 5 years ago

Kurt-Hetrick commented 6 years ago

this is mostly for things that I don't have direct control over.

  1. final reports. I'm probably going to have to do a liftover on the fly.
  2. bed files. I'm not sure about what to do here...I'm probably going to rely on the user to supply the right files. It will be pretty obvious when the wrong bed file is used.
Kurt-Hetrick commented 6 years ago
  1. annovar databases.
Kurt-Hetrick commented 6 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

Kurt-Hetrick commented 6 years ago

just a note to think about the modeled centromeres. possibly flag them in the vcf using heng li's repeat mask track.

Kurt-Hetrick commented 5 years ago

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.

Kurt-Hetrick commented 5 years ago

marking this as done