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Joint genotyping different caputre kits
Hello, I have ~35 exomes which I want to analyze following your best practices. Because 3 different capture kits were used to generate these data, I am wondering which is the right thing to do:
Option 1. Run the entire pipeline using a interval list with the union of the three different intervals.
Option 2. Run samples in three different batches (one for each capture kit used) and generate gVCF files. After this, do the joint genotyping and VSQR in all samples together.
Thanks a lot for your help,