Genome STRiP protocols

View Genome STRiP computational protocol

Genome STRiP statistics

You need an account to access this content

info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Structural variant detection Duplication detection Deletion detection CNV detection chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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


Add your version

Documentation


Maintainer


  • person_outline Steven McCarroll <>

Additional information


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

Publications for Genome STRucture In Populations

Genome STRiP in pipelines

 (3)
2017
PMCID: 5615344
PMID: 28837078
DOI: 10.3390/genes8090210

[…] (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 […]

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

[…] the three breeds, were studied in terms of population diversity, population structure, and population differentiation. population diversity was calculated using ‘variantspersampleannotator’ from ‘genome strip’ software, which provides distribution of variants across samples and populations. we performed principal component analysis (pca) using plink (v1.90p) software to distinguish three […]

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

[…] three known deletions from,,, qtl from qtldb. vcftools (v0.1.15) software and plink (v1.90p) software were used for analysing the vcf file., 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 […]

Genome STRiP in publications

 (21)
PMCID: 5955905
PMID: 29769526
DOI: 10.1038/s41467-018-04332-3

[…] as input and the five first principal components as covariates in a logistic regression implemented in plink., 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 […]

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

[…] 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 […]

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

[…] assembly of reads. however, approaches based on only one sequence signature could be constrained by high false discovery rate (fdr), hence we employed a population scale sv detection method called ‘genome structure in populations (genome strip)’—which leverages technical (e.g. rp and rd signals) and population-level sequence features (e.g. coherence around shared alleles, and heterogeneity […]

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

[…] and 13 370 deletions. the average number for each individual is 3102 ± 190. besides this, several other methods were then applied to call svs, including pindel [], cnvnator [], breakdancer [], and genome strip []. more detailed protocol information on sv calling can be found on the protocols.io platform []. we then merged all of the deletions in several sv sets according to their breakpoints […]

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

[…] of sequence similarity. the gene and regulatory content of the deletion was lifted from mouse ensembl genome browser., 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 […]

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).

Genome STRiP reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Genome STRiP