When I tried using only the assembler to call variants in a region, Platypus failed to make the call of an obvious variant right at the beginning of the region. Shifting the window by 15bp to the left (=k-mer length) enables it to call correctly.
We need to understand correctly what the exact problem is. Andy's thought is that it needs at least a k-mer length cover prior to the starting point of a var to be reported from the bubble graph.
When I tried using only the assembler to call variants in a region, Platypus failed to make the call of an obvious variant right at the beginning of the region. Shifting the window by 15bp to the left (=k-mer length) enables it to call correctly.
We need to understand correctly what the exact problem is. Andy's thought is that it needs at least a k-mer length cover prior to the starting point of a var to be reported from the bubble graph.