LUMPY protocols

LUMPY specifications

Information


Unique identifier OMICS_04674
Name LUMPY
Alternative names lumpy-sv, LUMPY Express
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data BAM
Operating system Unix/Linux
Programming languages C, C++, Python, Shell (Bash)
License MIT License
Computer skills Advanced
Version 0.2.13
Stability Stable
Requirements g++ compiler, CMake
Maintained Yes

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Documentation


Publication for LUMPY

LUMPY IN pipelines

 (3)
2015
PMCID: 4558871
PMID: 26254486
DOI: 10.1093/gbe/evv158

[…] appropriate genome. next, discordant paired-end and split-end reads were extracted from the bam files using samtools. these reads were then processed using the pairend_distro.py script from the lumpy suite to estimate the library size, mean, and standard deviation. the sample statistics of the library were then prepared as a configuration file with the following lumpy parameters to detect […]

2015
PMCID: 4558871
PMID: 26254486
DOI: 10.1093/gbe/evv158

[…] script from the lumpy suite to estimate the library size, mean, and standard deviation. the sample statistics of the library were then prepared as a configuration file with the following lumpy parameters to detect translocation events using two different libraries: 1) discordant paired-end library analysis: read length = 150; min nonoverlap = 150; discordant z = 4; back distance = […]

2015
PMCID: 4558871
PMID: 26254486
DOI: 10.1093/gbe/evv158

[…] were supported by reads with a minimum mapping quality of 40, had evidence from both paired-end and split-end read libraries, and had a minimum of six supporting reads., our analysis revealed that lumpy identified many breakpoints in which the host d. ananassae sequence corresponded to potential transposable elements (tes) (described further in results). to further characterize […]

LUMPY institution(s)
Department of Biochemistry and Molecular Genetics, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA; Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
LUMPY funding source(s)
Supported by an NIH/NHGRI award (1R01HG006693-01) and an NIH New Innovator Award (DP2OD006493-01) and a Burroughs Wellcome Fund Career Award.

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