The present disclosure provides a computer-implemented method for analyzing variants from a plurality of nucleic acid sequence reads using a computation pipeline, which comprises a module depending on a location-dependent parameter. The method comprises executing on a processor the steps of: receiving a plurality of nucleic acid sequence reads comprising at least a first nucleic acid sequence read and a second nucleic acid sequence read; mapping the first nucleic acid sequence read and the second nucleic acid sequence read to a first location and a second location in a genome, respectively; setting a first value and a second value for the location-dependent parameter on the basis of the first location and the second location in the genome, respectively; passing the first nucleic acid sequence read and the second nucleic acid sequence read through the module using the first value and the second value, respectively; and generating a variant call.