HapCUT specifications

Unique identifier:
OMICS_00198
Software type:
Package/Module
Restrictions to use:
None
Input format:
BAM, VCF
Operating system:
Unix/Linux
Version:
2.0
Maintained:
Yes
Alternative names:
HASH (Haplotype Assembly for Single Human), HapCUT2
Interface:
Command line interface
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.
Output data:
It outputs the phased haplotype blocks that can be assembled from the sequence reads.
Computer skills:
Advanced
Stability:
Stable

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HapCUT distribution

download

HapCUT support

Documentation

Maintainers

  • Vikas Bansal <>
  • Vikas Bansal <>

Additional information

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

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Publications

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

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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