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hapcut website  

HapCUT is a max-cut based algorithm for haplotype assembly that uses the mix of sequenced fragments from the two chromosomes of an individual, this program can be applied to sequence data generated from next-generation sequencing platforms. HapCUT takes as input the aligned SAM/BAM files for an individual diploid genome and the list of variants, and outputs the phased haplotype blocks that can be assembled from the sequence reads.

Required Modules


  • hapcut

System Variables

  • HPC_{{#uppercase:hapcut}}_DIR - installation directory