SNooPer specifications

Information


Unique identifier OMICS_14757
Name SNooPer
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data The normal and tumor files in SAMtools mpileup format for the training and calling phases, optional additional filters as BED files.
Output data The somatic p-value from the Fisher’s exact test, a categorical annotation of prediction (“PASS” or “REJ”) and associated class probability (from 0.5 to 1) for each somatic variant identified.
Biological technology Illumina
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.03
Stability Stable
Requirements Perl::Math::CDF, Text::NSP::Measures::2D::Fisher, Statistics::Test::WilcoxonRankSum, Statistics::R, Weka suite, R, Bedtools, JRE, pracma
Maintained Yes

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Maintainer


  • person_outline Jean-François Spinella <>

SNooPer article

SNooPer institution(s)
CHU Sainte-Justine Research Center, Université de Montréal, Montreal, Canada; Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montreal, Canada; Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Canada
SNooPer funding source(s)
This work was supported by research funds provided by the Terry Fox Research Institute and the Canadian Institutes for Health Research and by a Réseau de médecine génétique appliquée (RMGA) Fellowship.

SNooPer review

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Mike_D

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Desktop
Very useful tool for my data