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GSR: Simulator - BAMSurgeon
| 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 | 8 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, 07-01-2015 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | 11-10-2017 (2346 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. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Diploid DNA Sequence, Haploid DNA Sequence, Sex Chromosomes, Mitochondrial DNA, |
| 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 | |
| Spatiality | |
| 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, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
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]