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BAMSurgeon specifications

Information


Unique identifier OMICS_06796
Name BAMSurgeon
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data An indexed reference genome, a pre-existing file and a list of intervals along with the SV type and parameters.
Input format PY+BAM
Biological technology Illumina
Operating system Unix/Linux
Programming languages Python, Shell (Bash)
License MIT License
Computer skills Advanced
Version 1.0.0
Stability Stable
Requirements
samtools/wgsim/tabix, pysam, bwa, velvet, exonerate, picard
Maintained Yes

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Documentation


Maintainers


  • person_outline Paul Boutros
  • person_outline Adam Ewing

Publications for BAMSurgeon

BAMSurgeon citations

 (9)
library_books

A review of somatic single nucleotide variant calling algorithms for next generation sequencing data

2018
Comput Struct Biotechnol J
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] simulators with built-in or user-supplied error models such as art  and seqmaker . alternatively, hybrid datasets featuring real reads and simulated variants at arbitrary vafs can be generated using bamsurgeon . synthetic reads can be generated in large scale, at virtually no cost, and most importantly, contain known variants. however, synthetic data alone are generally considered inadequate […]

library_books

Germline contamination and leakage in whole genome somatic single nucleotide variant detection

2018
BMC Bioinformatics
PMCID: 5793408
PMID: 29385983
DOI: 10.1186/s12859-018-2046-0

[…] of the synthetic tumours and their properties are fully detailed in ewing et al. []. briefly, high coverage binary alignment map (bam) files were obtained from cell lines hcc1143 and hcc1954 []. bamsurgeon [] was used to randomly ‘spike-in’ germline mutations into the bam files. each file was then split into two: one file representing a synthetic tumour and the other file representing […]

library_books

Improving somatic variant identification through integration of genome and exome data

2017
BMC Genomics
PMCID: 5657037
DOI: 10.1186/s12864-017-4134-3

[…] somatic mutations were generated on chromosome 1 of individual “a0bw” from tcga []. the whole genome had 30x coverage and the whole exome had 150x coverage. somatic mutations were generated using bamsurgeon [] at different depths and different allele fractions on whole genome and whole exome platforms (see methods for details)., the somatic mutations that are generated by bamsurgeon […]

library_books

Natural Variation in the Distribution and Abundance of Transposable Elements Across the Caenorhabditis elegans Species

2017
Mol Biol Evol
PMCID: 5850821
PMID: 28486636
DOI: 10.1093/molbev/msx155

[…] true and the minimum percent id set to 0.70. the ability of these programs to detect new insertions of transposons relative to the reference genome was assessed by running the programs after using bamsurgeon (github.com/adamewing/bamsurgeon) to simulate 1,000 sequences of tes in an n2 bam file in regions without pre-existing transposons and without excessive coverage (>1,000× coverage). […]

library_books

Quantitation of Murine Stroma and Selective Purification of the Human Tumor Component of Patient Derived Xenografts for Genomic Analysis

2016
PLoS One
PMCID: 5017757
PMID: 27611664
DOI: 10.1371/journal.pone.0160587

[…] second technical replicate was aligned to the hybrid genome, and downsampled to 60× doc. to generate a virtual tumor, a completely known mutation profile was then introduced by bam replacement using bamsurgeon and the is3 mutation set from the icgc-tcga dream somatic mutation calling challenge at a range of variant allele frequencies []. wgss data from the nsg mouse strain generated […]

library_books

The Genetic Basis of Natural Variation in Caenorhabditis elegans Telomere Length

2016
Genetics
PMCID: 5012401
PMID: 27449056
DOI: 10.1534/genetics.116.191148

[…] to determine which type of single-nucleotide-variant (snv) caller would perform best on our dataset and to set appropriate filters, we simulated variation in the n2 background. we used bamsurgeon (http://github.com/adamewing/bamsurgeon), which modifies base calls to simulate variants at specific positions within aligned reads and then realigns reads to the reference genome using […]


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BAMSurgeon institution(s)
Ontario Institute for Cancer Research; Toronto, ON, Canada; Department of Biomolecular Engineering; University of California, Santa Cruz; Santa Cruz, CA, USA; Mater Research Institute; University of Queensland; Woolloongabba, QLD, Australia; Computational Biology Program; Oregon Health & Science University; Portland, OR, USA; Sage Bionetworks; Seattle, WA, USA; Department of Bioinformatics and Computational Biology; University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genetics; University of Alabama at Birmingham; Birmingham, AL, USA; Informatics Institute; University of Alabama at Birmingham; Birmingham, AL, USA; IBM Computational Biology Center; T.J.Watson Research Center; Yorktown Heights, NY, USA; Department of Medical Biophysics; University of Toronto; Toronto, ON, Canada; Department of Pharmacology & Toxicology; University of Toronto; Toronto, ON, Canada
BAMSurgeon funding source(s)
Supported by the Ontario Institute for Cancer Research through funding provided by the Government of Ontario, Prostate Cancer Canada, the Movember Foundation - Grant #RS2014-, Movember funds through Prostate Cancer, Genome Canada through a Large-Scale Applied Project contract, the Discovery Frontiers: Advancing Big Data Science in Genomics Research program, which is jointly funded by the Natural Sciences and Engineering Research Council (NSERC) of Canada, the Canadian Institutes of Health Research (CIHR), Genome Canada, and the Canada Foundation for Innovation (CFI), a Terry Fox Research Institute New Investigator Award and a CIHR New Investigator Award, a CIHR Computational Biology Undergraduate Summer Student Health Research Award, an Australian Research Council Discovery Early Career Researcher Award DE150101117, the Mater Foundation and National Institutes of Health (NIH) grants: R01-CA180778 and U24-CA143858.

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