ALoFT specifications

Unique identifier:
OMICS_20746
Software type:
Pipeline/Workflow
Restrictions to use:
None
Output data:
A list of formatted information calculated by VAT and features calculated by ALoFT; a tab-delineated file and includes extensive annotations for premature stop variants and frameshift-causing indels; a tab-delineated file and includes extensive annotations for variants affecting canonical splice sites.
Operating system:
Unix/Linux
Computer skills:
Advanced
Stability:
Stable
Name:
Annotation of Loss-of-Function Transcripts
Interface:
Command line interface
Input format:
VCF
Output format:
VCF, TSV
Programming languages:
Perl, Python, R
Version:
1.0
Maintained:
Yes

versioning

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ALoFT distribution

download

ALoFT support

Maintainers

  • Mark Gerstein <>
  • Suganthi Balasubramanian <>

Additional information

http://aloft.gersteinlab.org/documentation/#usage

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Publications

Institution(s)

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Molecular Biophysics and Biochemistry Department, Yale University, NH, CT, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Computer Science, Yale University, NH, CT, USA; Regeneron Genetics Center, Tarrytown, NY, USA; Bina Technologies, Part of Roche Sequencing, Belmont, CA, USA

Funding source(s)

Supported by grants 5R01GM104371 (US National Institutes of Health/National Institute of General Medical Sciences), and U54HG006504 (Yale Center for Mendelian Genomics).

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