The Frontline Support team will be slow to respond December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks. Happy Holidays!
Is it advisable to use multiple different types of cancer subtypes for joint variant calling?
I am running GATK on multiple breast cancer cell line subtypes. I was wondering if it would be advisable to call the variants on them together as well as doing their joint genotyping. If not what is the best practice of using genotyping on individual lines.