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Genome STRiP specifications


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


No version available



  • person_outline Steven McCarroll

Additional information

Publications for Genome STRucture In Populations

Genome STRiP citations


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

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 […]


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

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 […]


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

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 ( […]


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

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 […]


Deep whole genome sequencing of 90 Han Chinese genomes

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) […]


Genomes of the Mouse Collaborative Cross

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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