GSR: Simulator - BAMSurgeon

Basic Package Attributes
AttributeValue
Title BAMSurgeon
Short Description Methods for realistic simulation of mutations in real data.
Long Description BAMSurgeon can add SNVs, INDELs, and several forms of structural variant (SV) to existing BAM files and using multiple alignment methods, which is useful for testing mutation detection software in a variety of contexts.
Version 1.0
Project Started 2012
Last Release 5 years, 3 months ago
Homepagehttps://github.com/adamewing/bamsurgeon
Citations Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, Bare JC, P'ng C, Waggott D, Sabelnykova VY, Kellen MR, et al., Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection., Nat Methods, 07-01-2015 [ Abstract, cited in PMC ]
GSR CertificationGSR-certified

Accessibility
Documentation
Application
Support

Last evaluated11-10-2017 (1071 days ago)
Author verificationThe basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataDiploid DNA Sequence, Haploid DNA Sequence, Sex Chromosomes, Mitochondrial DNA,
VariationsSingle Nucleotide Variation, Insertion and Deletion, Inversion and Rearrangement, Genotype or Sequencing Error,
Simulation MethodResample Existing Data, Other,
Input
Data TypeOther,
File formatOther,
Output
Data TypeGenotype or Sequence, Mutation,
Sequencing Reads
File FormatVCF, SAM or BAM,
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size Changes
Gene Flow
Spatiality
Life Cycle
Mating System
Fecundity
Natural Selection
Determinant
Models
Recombination
Mutation Models
Events Allowed
Other
InterfaceCommand-line,
Development
Tested PlatformsMac OS X, Linux and Unix,
LanguagePython,
LicenseOther,
GSR CertificationAccessibility, Documentation, Application, Support,

The following 2 publications are selected examples of applications that used BAMSurgeon.

2014

Radenbaugh AJ, Ma S, Ewing A, Stuart JM, Collisson EA, Zhu J, Haussler D, RADIA: RNA and DNA integrated analysis for somatic mutation detection., PLoS One, 01-01-2014 [Abstract]

2013

Ewing AD, Ballinger TJ, Earl D, Harris CC, Ding L, Wilson RK, Haussler D, Retrotransposition of gene transcripts leads to structural variation in mammalian genomes., Genome Biol, 03-13-2013 [Abstract]


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