A system for improving variant call accuracy by executing Hidden Markov Model analysis on genetic sequence data, the genetic sequence data including a plurality of reads of genomic sample sequence data generated by a sequencer and reference sequence data comprising haplotype sequence data, each of the reads of genomic sample sequence data and the haplotype sequence data comprising a sequence of nucleotides, the system comprising: an HMM accelerator comprising a plurality of HMM processing clusters and a data distributor; one or more processing units; one or more first memories for storing (i) the plurality of reads and (ii) the reference sequence data,; and one or more second memories for storing computer instructions that, when executed by the one or more processing units, cause the one or more processing units to: identify an active region within the plurality of reads, wherein the active region is identified as being a source of variation between one or more reads and the reference sequence data; provide, to the data distributor, one or more jobs to be performed on the one or more reads of the active region, wherein the one or more jobs correspond to a subset of an HMM analysis, wherein the data distributor is configured to distribute the one or more jobs to an HMM processing cluster of the plurality of HMM processing clusters; wherein the HMM accelerator further comprises: an integrated circuit formed of one or more hardwired digital logic circuits that are interconnectable by a plurality of physical electrical interconnects, wherein one or more of the plurality of physical electrical interconnects comprises a memory interface for the integrated circuit to access the one or more first memories, the hardwired digital logic circuits including at least a first subset of digital logic circuits programmed to implement the plurality of HMM clusters, wherein each HMM cluster includes a set of processing engines, and wherein a first set of processing engines of a first HMM cluster of the plurality of HMM clusters is configured to: obtain, from the data distributor, one or more jobs; perform a subset of the HMM analysis on at least some of the reads in the plurality of reads in the active region; and determine, based on the performed subset of the HMM analysis, HMM result data indicating the likelihood of each read in the plurality of reads being associated with a haplotype of the haplotype sequence data; wherein the plurality of physical electrical interconnects comprise an output from the integrated circuit for communicating the HMM result data produced by the first HMM cluster. an HMM accelerator comprising a plurality of HMM processing clusters and a data distributor; one or more processing units; one or more first memories for storing (i) the plurality of reads and (ii) the reference sequence data,; and one or more second memories for storing computer instructions that, when executed by the one or more processing units, cause the one or more processing units to: identify an active region within the plurality of reads, wherein the active region is identified as being a source of variation between one or more reads and the reference sequence data; provide, to the data distributor, one or more jobs to be performed on the one or more reads of the active region, wherein the one or more jobs correspond to a subset of an HMM analysis, identify an active region within the plurality of reads, wherein the active region is identified as being a source of variation between one or more reads and the reference sequence data; provide, to the data distributor, one or more jobs to be performed on the one or more reads of the active region, wherein the one or more jobs correspond to a subset of an HMM analysis, wherein the data distributor is configured to distribute the one or more jobs to an HMM processing cluster of the plurality of HMM processing clusters; wherein the HMM accelerator further comprises: an integrated circuit formed of one or more hardwired digital logic circuits that are interconnectable by a plurality of physical electrical interconnects, wherein one or more of the plurality of physical electrical interconnects comprises a memory interface for the integrated circuit to access the one or more first memories, the hardwired digital logic circuits including at least a first subset of digital logic circuits programmed to implement the plurality of HMM clusters, wherein each HMM cluster includes a set of processing engines, and wherein a first set of processing engines of a first HMM cluster of the plurality of HMM clusters is configured to: obtain, from the data distributor, one or more jobs; perform a subset of the HMM analysis on at least some of the reads in the plurality of reads in the active region; and determine, based on the performed subset of the HMM analysis, HMM result data indicating the likelihood of each read in the plurality of reads being associated with a haplotype of the haplotype sequence data; obtain, from the data distributor, one or more jobs; perform a subset of the HMM analysis on at least some of the reads in the plurality of reads in the active region; and determine, based on the performed subset of the HMM analysis, HMM result data indicating the likelihood of each read in the plurality of reads being associated with a haplotype of the haplotype sequence data; wherein the plurality of physical electrical interconnects comprise an output from the integrated circuit for communicating the HMM result data produced by the first HMM cluster.