I am a bit confused as to the steps for GATK g-CNV and therefore I am making this post to understand it. I am dealing with multiple .bams as an input (so I believe I am supposed to use cohort mode). Are the following a correct set of steps to use for exome data:
Or would it be better to do:
or am I reading the documentation (https://gatk.broadinstitute.org/hc/en-us/articles/360035531152) incorrectly? Is there another way to do these steps?
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