BAMSurgeon

Basic Package Attributes
Attribute	Value
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	2 years, 9 months ago
Homepage	https://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, July 1, 2015 [Abstract, cited in PMC ]
GSR Certification	✔Accessibility ✔Documentation ✔Application ✔Support
Last certified	July 12, 2015 (999 days ago)
Author verification	The 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 Category	Attribute
Target
Type of Simulated Data	Diploid DNA Sequence, Haploid DNA Sequence, Sex Chromosomes, Mitochondrial DNA,
Sequencing Reads
Variations	Single Nucleotide Variation, Insertion and Deletion, Inversion and Rearrangement, Genotype or Sequencing Error,
Simulation Method	Resample Existing Data, Other,
Input
Data Type	Other,
File format	Other,
Output
Data Type	Genotype or Sequence, Mutation,
Sequencing Reads
File Format	VCF, SAM or BAM,
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size Changes
Gene Flow
Life Cycle
Mating System
Fecundity
Natural Selection
Determinant
Models
Recombination
Mutation Models
Events Allowed
Other
Interface	Command-line,
Development
Tested Platforms	Mac OS X, Linux and Unix,
Language	Python,
License	Other,
GSR Certification	Accessibility, Documentation, Application, Support,

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

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, Jan. 1, 2014 [Abstract]

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, March 13, 2013 [Abstract]