Genome STRiP statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Genome STRiP
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Tool usage distribution map

This map represents all the scientific publications referring to Genome STRiP per scientific context
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Associated diseases

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Popular tool citations

chevron_left Structural variant detection CNV detection Deletion detection Duplication detection chevron_right
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Genome STRiP specifications

Information


Unique identifier OMICS_05101
Name Genome STRiP
Alternative name Genome STRucture In Populations
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability Stable
Registration required Yes
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Steven McCarroll

Additional information


http://software.broadinstitute.org/software/genomestrip/index.html

Publications for Genome STRucture In Populations

Genome STRiP citations

 (18)
library_books

A whole genome sequence study identifies genetic risk factors for neuromyelitis optica

2018
Nat Commun
PMCID: 5955905
PMID: 29769526
DOI: 10.1038/s41467-018-04332-3

[…] We discovered and genotyped CNVs in the Stage I WGS data using the CNV pipeline of Genome STRiP. In brief, Genome STRiP’s CNV pipeline genotypes segments of the genome using observed read depth-of-coverage by fitting a Gaussian Mixture Model constrained to call integer copy numbers […]

library_books

Common α globin variants modify hematologic and other clinical phenotypes in sickle cell trait and disease

2018
PLoS Genet
PMCID: 5891078
PMID: 29590102
DOI: 10.1371/journal.pgen.1007293

[…] f genetic ancestry were calculated for each participant from the sequence data.[] A subset of 3,009 JHS TOPMed participants underwent genotyping for the α-globin copy number variation (CNV) using the Genome STRiP multi-sample structural variant calling algorithm[] and were eligible for the current analysis. We further excluded 6 individuals for low-quality CNV calls, 3 individuals who were homozyg […]

library_books

Genome wide mapping of large deletions and their population genetic properties in dairy cattle

2017
PMCID: 5824824
PMID: 28985340
DOI: 10.1093/dnares/dsx037

[…] Deletion discovery and genotyping were carried out using Genome STRiP. After filtering, we report 8,480 large deletions with genotypes in 67 Holsten, 27 Jersey, and 81 Nordic Red Cattle. The deletion size ranged from 199 bp to 773 KB with a mean of 4.5 KB ( […]

library_books

Whole Genome Sequencing Revealed Mutations in Two Independent Genes as the Underlying Cause of Retinal Degeneration in an Ashkenazi Jewish Pedigree

2017
Genes
PMCID: 5615344
PMID: 28837078
DOI: 10.3390/genes8090210

[…] morphism (SNPs), short insertion-deletion (INDELs) and single nucleotide variant (SNVs) calling was performed using Genome Analysis Tool Kit (GATK) []. Copy number variations (CNVs) were called using Genome STRiP and SpeedSeq software []. Variants were filtered to detect rare potentially deleterious variants segregating with disease. Rare deleterious SNVs were extracted based on the frequency of a […]

library_books

Deep whole genome sequencing of 90 Han Chinese genomes

2017
GigaScience
PMCID: 5603764
PMID: 28938720
DOI: 10.1093/gigascience/gix067

[…] nese_genomesOperating system(s): LinuxProgramming language: Shell, Perl, Java, and C++Other requirements: BWA, 0.6.1; SOAPsv, 1.02; SOAPdenovo2; PINDEL, 0.2.4t; cnvnator, 0.2.7; Breakdancer-max, 1.2; Genome STRIP, v. 1.0; SAMtools, 0.1.18; Picard, 1.61; GATK, 2.7; BEAGLE, v. 3License: GNU General Public License v.3.0 (GPLv3) […]

library_books

Genomes of the Mouse Collaborative Cross

2017
Genetics
PMCID: 5499171
PMID: 28592495
DOI: 10.1534/genetics.116.198838

[…] The Picard MarkDuplicates processed alignment files were used as an input to Genome STRiP 2.0 () for copy number variation (CNV) discovery. Ploidy map and reference files (prerequisite for Genome STRiP) were constructed from mouse reference genome (mm10). We used the tiling wi […]


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Genome STRiP institution(s)
Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA; Digital Biology Center, Bio-Rad Laboratories, Inc., Pleasanton, CA, USA
Genome STRiP funding source(s)
Supported by a grant from the National Human Genome Research Institute (R01 HG006855) and an additional grant from NHGRI (U01 HG006510).

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