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broadinstitute / gatk-sv

A structural variation pipeline for short-read sequencing
BSD 3-Clause "New" or "Revised" License
160 stars 71 forks source link

MEI to be calculated in MainVcfQc #667

Open xuefzhao opened 2 months ago

xuefzhao commented 2 months ago

Shall we consider adding mobile element insertions as independent variant type in MainVcfQc?

mwalker174 commented 3 weeks ago

It could certainly be helpful for QC purposes. However, for the purposes of comparison to other call sets or presentations it might not be desirable. Perhaps a toggle option would work.