VarDict represents complex variant composites as a single variant, rather than as multiple individual variants. Whenever an InDel is detected in a read, VarDict will recursively scan for another InDel (within 10 bp)
or mismatches (within 3 bp) in the same read, and if found,
combines them as one variant. The same rule also applies
to consecutive mismatches, resulting in calling multiple nucleotide variants (MNVs).
how can I see a germline or simatic variant is in the same read?
thanks a lot
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