ALoFT specifications


Unique identifier OMICS_20746
Name ALoFT
Alternative name Annotation of Loss-of-Function Transcripts
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format VCF
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.
Output format VCF, TSV
Operating system Unix/Linux
Programming languages Perl, Python, R
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes



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  • person_outline Mark Gerstein <>
  • person_outline Suganthi Balasubramanian <>

Additional information

Publication for Annotation of Loss-of-Function Transcripts

ALoFT 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
ALoFT 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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