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Haplotype Amplification in Tumor Sequences HATS

A tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next-generation sequencing tumor data. The amplified haplotype may reveal gene variants. We assess the performance of HATS using simulated amplified regions generated from varying copy number and coverage levels, followed by amplicons in real data. We demonstrate that HATS infers the amplified alleles more accurately than does the naive approach, especially at low to intermediate coverage levels and in cases (including high coverage) possessing stromal contamination or allelic bias.

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HATS classification

HATS specifications

Software type:
Application/Script
Restrictions to use:
None
Programming languages:
Java
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux
License:
Academic Free License version 3.0, GNU General Public License version 2.0
Stability:
Stable

HATS distribution

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HATS support

Maintainer

  • Itsik Pe'er <>

Credits

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Publications

Institution(s)

Department of Biomedical Informatics, Columbia University, New York, NY, USA; Department of Computer Science, Columbia University, New York, NY, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Medical and Population Genetics Program, The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Genetics, Case Western Reserve University School of Medicine, Cleveland, OH, USA

Funding source(s)

This work was supported by the National Institutes of Health and National Library of Medicine (5T15 LM007079-14 to the Medical Informatics Research Training Program, Department of Biomedical Informatics, Columbia University); and the National Institutes of Health (1 R01 CA131341-01A1).

Link to literature

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