The assumption of HMM model is the dependence between current state and previous state. On small panel (hundreds of genes), the gap between targeted regions is too large to presume this dependence. In such case, is HMM based CNV calling still valid?

  • $\begingroup$ Difference in what? What HMM based calling method? Will you be looking at the depth of coverage? Split reads? Something else? Is this about using XHMM? CNV calling on panels or exomes is not the best approach in general, largely because the targets are so far apart. But why would that affect an HMM-based approach any more? The transition can still be measured from "looks like CNV" to "doesn't look like CNV". $\endgroup$ – terdon Aug 20 '19 at 8:18

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