Karyotyping Pipeline for Identifying duplicated chromosomes

Question

[Evan]

I'm looking for recommendations on tools for identifying extra chromosomes from exome data. In this case we have a large quantity of sequencing runs that we would like to re analyze to identify if there are any samples that have extra chromosomes. We also have full variant calls on all the samples so if there is a route for doing deeper analysis on the VCFs to identify this then that is also a route we can take