Methods for realistic simulation of mutations in real data. Long Description (required)
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. https://github.com/adamewing/bamsurgeon adam.ewing@mater.uq.edu.au
Step 1: Use the attribute tree to add new attributes or remove pre-selected attributes to describe the simulator.
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Summary of Proposed Changes Step 2: Review list of proposed attribute addition(s) and subtraction(s).
Can't Find the Attribute You Are Looking For? If you would like to propose an attribute that you cannot find in the tree above, or if you would like to add a clarification to one or more attributes for this simulator (e.g. a specific file format for attribute /Output/File Format/Other), please list them in the Additional Comment box of the Submit tab .
Summary of Proposed Changes Current Citations/Applications
[Pubmed ID: 23497673 ],
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 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=23497673, , Application
[Pubmed ID: 25405470 ],
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 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=25405470, , Application
[Pubmed ID: 25984700 ],
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 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=25984700, Primary Citation