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Is 70k millions variants for WES trios enough?
I am using GATK for trio analysis of WES data where I have proband and parents. I would like to execute a Joint analysis of all the 50 families that I have but could not get more than about 70 thousands variants.
How can I fix this?
My target is the clinical_exome from Agilent (about 50millions bp) and coverage of samples is very high (100-200X).
Can you help me in locating where do I have a mistake in the analysis?