DeepSNVMiner specifications

Unique identifier:
OMICS_12087
Interface:
Command line interface
Input data:
DeepSNVMiner requires three input files; paired-end FASTQ read files and a BED file containing the specific locations of targeted genomic region(s). An initial configuration step is also required to determine the location of three required external resources; Burrows-Wheeler Aligner (BWA), SAMtools, and a reference genome FASTA file with BWA index files.
Operating system:
Unix/Linux, Mac OS
Computer skills:
Advanced
Maintained:
Yes
Software type:
Pipeline/Workflow
Restrictions to use:
Academic or non-commercial use
Output data:
The final report contains a listing of all variants detected, based on either the user-configured expected variant frequency or default parameters.
Programming languages:
Perl
Stability:
Stable

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DeepSNVMiner support

Documentation

Maintainer

  • Matthew A. Field <>

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Publications

Institution(s)

Department of Immunology, John Curtin School of Medical Research, Australian National University, Canberra, Australia; National Computational Infrastructure, Canberra, Australia; School of Medicine and Pharmacology, University of Western Australia, Harry Perkins Institute, Perth, Australia; Haematology Translational Research Unit, Haematology Unit, ACT Pathology, Canberra, Australia; ANU Medical School, Australian National University, Canberra, Australia; Immunology Division, Garvan Institute of Medical Research, Sydney, Australia; St Vincent’s Clinical School, University of New South Wales, Darlinghurst, Australia

Funding source(s)

National Institutes of Health Grant U19 AI100627; NHMRC Australian Fellowship 585490; Bioplatoforms Australia

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