HapCUT specifications


Unique identifier OMICS_00198
Name HapCUT
Alternative names HASH (Haplotype Assembly for Single Human), HapCUT2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A file for an individual containing reads aligned to a reference genome and a file containing SNVs for the individual with respect to the reference.
Input format BAM, VCF
Output data It outputs the phased haplotype blocks that can be assembled from the sequence reads.
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes



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  • person_outline Vikas Bansal <>
  • person_outline Vikas Bansal <>

Additional information

Previous version: https://github.com/vibansal/hapcut

Publications for HapCUT

HapCUT institution(s)
Department of Computer Science & Engineering, University of California, San Diego, La Jolla CA, USA; Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
HapCUT funding source(s)
Supported in part by a grant from the NIH (HG007430, HG007836 and GM114362) and NSF (DBI-1458557, IIS-1318386).

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