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if two variant are side by side,will gatk try to merge them?

hi, image there is A -> T in position 2, and A -> G in position 3 or A -> NONE ,
will gatk try to merge(the combination can be snp+snp, snp+indel, indel+indel), because different combination or single alone can generate a totally different amino change, and finaly impact the drug instruction.

VarScan will merge some variants if it think ok, but also give single alone variant

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