LUMPY protocols

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chevron_left Structural variant detection Deletion detection Duplication detection Inversion detection CNV detection chevron_right
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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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Publication for LUMPY

LUMPY in pipelines

 (4)
2017
PMCID: 5499169
PMID: 28450459
DOI: 10.1534/genetics.116.198895

[…] a maximum of 16. complete sequencing data for all of these clones is available under ncbi bioproject prjna339148, biosample accessions samn05729740-5729793. structural variants were called using lumpy (version accessed on july 6, 2016) (), and copy number variants were called using dnacopy (version accessed on july 21, 2016) () on 1000 bp windows of coverage across the genome., the deletion […]

2016
PMCID: 4938650
PMID: 27172215
DOI: 10.1534/g3.116.029504

[…] on paired-end read mapping. in contrast, pindel splits the unmapped end of a one-end anchored read into a few pieces, and performs local realignment of each piece in the candidate region. finally, lumpy incorporates both split read analysis and read-pair discordance to detect breakpoints. to evaluate the accuracy of the predicted breakpoints, 20 randomly selected deletion and inversion […]

2016
PMCID: 5381350
PMID: 28011720
DOI: 10.1093/dnares/dsw050

[…] or both, can be set for detection. the small variations are called with samtools through an accurate and sensitive double calling step, while the structural variants are detected using lumpy (version 0.0.11; options used: -mv 4 –tt 0 –pe –sr)., once the variant calling step has been successfully completed, statistics on sequence capture experiment are calculated. the statistics […]

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 […]


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LUMPY in publications

 (43)
PMCID: 5885317
PMID: 29618373
DOI: 10.1186/s13071-018-2817-5

[…] major enzyme families: glutathione s-transferases, cytochrome p450 monooxygenases and esterases., 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 paired_distro.py script from lumpy. […]

PMCID: 5862875
PMID: 29563506
DOI: 10.1038/s41408-018-0062-y

[…] using bwa. acquired snvs were called in each tumor sample relative to its paired normal sample using samtools, somaticsniper, mutect, strelka, and varscan2 (ref. ). translocations were called using lumpy, with results filtered by a machine learning approach optimized to achieve high precision relative to available fish results. cnvs were called using copycat2 (https://github.com/abelhj/cc2/; […]

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

[…] specific to centromere 15 (d15z1, tig00007244)., using svtyper and platinum illumina wgs alignments, we genotyped 2,414 gm12878 structural variants (svs), which were previously identified using lumpy and validated with pacbio and/or moleculo reads. we then genotyped the same svs using alignments of our nanopore reads from the 30×-coverage data set and a modified version of svtyper. […]

PMCID: 5780461
PMID: 29362391
DOI: 10.1038/s41598-018-19782-4

[…] with default options. summary statistics on coverage obtained and reads mapped per sire can be found in supplementary table . cnv calling was carried out based on speedseq, which incorporates lumpy and cnvnator for cnv detection. calls with length <1 kb or 1 mb were excluded. in accordance with the application guidelines, a q0-filter of 0.5 for cnvnator and a minimum quality threshold […]

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

[…] 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 […]


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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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