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LUMPY specifications


Unique identifier OMICS_04674
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
g++ compiler, CMake
Maintained Yes




No version available


Publication for LUMPY

LUMPY citations


Genetic variation associated with increased insecticide resistance in the malaria mosquito, Anopheles coluzzii

PMCID: 5885317
PMID: 29618373
DOI: 10.1186/s13071-018-2817-5
call_split See protocol

[…] Structural variants were detected in whole genome sequencing data (Additional file : Table S4) using LUMPY version 0.2.13 []. Discordant paired-end and split-end reads were extracted using samtools. Library size, mean, and standard deviation were estimated using script from LUMPY. Th […]


FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods

Genome Biol
PMCID: 5859555
PMID: 29559002
DOI: 10.1186/s13059-018-1404-6

[…] with the 1000GP Phase 3 SV callset [, , ]. For Jaccard similarity, FusorSV outperformed all individual algorithms (40%) with MetaSV as the next best method (32%), followed by BreakDancer, BreakSeq2, LUMPY, DELLY, and Hydra (all near 20%).Fig. 4For duplication calls, GenomeSTRiP performed at 26% precision and 14% recall, while CNVnator performed at 22% precision and 3% recall. The MetaSV duplicati […]


Chromothripsis and ring chromosome 22: a paradigm of genomic complexity in the Phelan McDermid syndrome (22q13 deletion syndrome)

J Med Genet
PMCID: 5869459
PMID: 29378768
DOI: 10.1136/jmedgenet-2017-105125

[…] tting the average coverage of 1000 bp windows sliding over the whole chromosome length, in order to identify large deletions and duplications in each chromosome. Structural variants were called using Lumpy (V.0.2.12) and Manta (V.0.29.6). Then these structural variants were visualised and manually checked in Integrative Genomics Viewer (IGV) genome browser (V.2.3.72) in order to reconstruct chromo […]


Nanopore sequencing and assembly of a human genome with ultra long reads

Nat Biotechnol
PMCID: 5889714
PMID: 29431738
DOI: 10.1038/nbt.4060

[…] Previously identified high-confidence GM12878 SVs, validated with Moleculo and/or PacBio long reads, were used to determine genotyping sensitivity. Using LUMPY, we recalled SVs in the Platinum Genomes NA12878 Illumina data set (paired-end reads; European Nucleotide Archive, Run Accession ERR194147), intersected these calls with the aforementioned high […]


GLS loss of function causes autosomal recessive spastic ataxia and optic atrophy

PMCID: 5817843
PMID: 29468182
DOI: 10.1002/acn3.522

[…] ed homozygous regions present in both siblings (Fig. B). With the hypothesis that the disease‐causing mutation could be a copy number variant or structural rearrangement, we used the software program LUMPY, to analyze the WGS data on Patient 1. We limited our analysis to CNVs found within the linked homozygous regions that overlapped with the coding region of a gene, and were therefore likely to h […]


Forward genetics screen coupled with whole genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger

Appl Microbiol Biotechnol
PMCID: 5794824
PMID: 29305699
DOI: 10.1007/s00253-017-8717-3

[…] al. ). Structural variations such as insertion, deletion, or duplication of relatively large segments were identified using Pindel (Ye et al. ), BreakDancer (Chen et al. ), Delly (Rausch et al. ), or Lumpy (Layer et al. ). […]


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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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