SNooPer specifications

Unique identifier:
OMICS_14757
Software type:
Package/Module
Restrictions to use:
Academic or non-commercial use
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.
Operating system:
Unix/Linux
License:
GNU General Public License version 3.0
Version:
0.03
Requirements:
Perl::Math::CDF, Text::NSP::Measures::2D::Fisher, Statistics::Test::WilcoxonRankSum, Statistics::R, Weka suite, R, Bedtools, JRE, pracma
Name:
SNooPer
Interface:
Command line interface
Input data:
The normal and tumor files in SAMtools mpileup format for the training and calling phases, optional additional filters as BED files.
Biological technology:
Illumina
Programming languages:
Perl
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes

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SNooPer distribution

download

SNooPer support

Maintainer

  • Jean-François Spinella <>

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Credits

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Publications

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

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.

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Mike_D

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Very useful tool for my data

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