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Protocols

IGV specifications

Information


Unique identifier OMICS_00917
Name IGV
Alternative names Integrative Genomics Viewer, IGVtools, Integrated Genome Viewer
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Mac OS, Windows
Programming languages Java
License GNU Lesser General Public License version 3.0, MIT License
Computer skills Medium
Version 2.4.8
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainers


  • person_outline James Robinson <>
  • person_outline IGV Team <>

Additional information


http://software.broadinstitute.org/software/igv/UserGuide

Publications for Integrative Genomics Viewer

IGV citations

 (1849)
call_split

Mutations in six nephrosis genes delineate a pathogenic pathway amenable to treatment

2018
PMCID: 5958119
PMID: 29773874
DOI: 10.1038/s41467-018-04193-w
call_split See protocol

[…] technologies). libraries were sequenced on a miseq or hiseq2000 (illumina). mapping and variant call were performed using surecall v2.1.0.21. variants in itsn2 were manually verified using an integrative genomics viewer (igv), and nonsynonymous mutations were retained and filtered for a maf < 0.01 in the 1000 genomes database and hgvd., sequence reads were mapped against the human […]

library_books

Methionine metabolism influences genomic architecture and gene expression through H3K4me3 peak width

2018
PMCID: 5955993
PMID: 29769529
DOI: 10.1038/s41467-018-04426-y

[…] all box plots, the boxes extend between the 25th and 75th percentiles, the center line shows the median, and the whiskers represent the minimal and maximal values. chip-seq tracks were created using integrative genomics viewer (http://software.broadinstitute.org/software/igv/)., codes are available at github page of the locasale lab (https://github.com/locasalelab/h3k4me3_met_restriction)., […]

library_books

Systematic pan cancer analysis of somatic allele frequency

2018
PMCID: 5956099
PMID: 29769535
DOI: 10.1038/s41598-018-25462-0

[…] counts for all the variant positions in all four datasets (normal exome, normal transcriptome, tumor exome and tumor transcriptome). selected read count assessments were visually examined using integrative genomics viewer. we excluded from further analyses variants which (1) were covered with less than 10 sequencing reads in the tumor dna or the rna sequencing data; (2) reside in known […]

library_books

Outlier response to anti PD1 in uveal melanoma reveals germline MBD4 mutations in hypermutated tumors

2018
PMCID: 5951831
PMID: 29760383
DOI: 10.1038/s41467-018-04322-5

[…] an ad/dp ratio of <0.05 and/or a population frequency higher than 1% (popfreq_all >0.01) were filtered out. all somatic mutations called by this procedure were controlled manually using the integrative genomics viewer (igv)., sashimi plots were generated with the r software version 3.4.2 and its packages genomicalignments (1.12.2) and genomicranges (1.28.4) from data downloaded […]

library_books

Complete mitochondrial and rDNA complex sequences of important vector species of Biomphalaria, obligatory hosts of the human infecting blood fluke, Schistosoma mansoni

2018
PMCID: 5943310
PMID: 29743617
DOI: 10.1038/s41598-018-25463-z

[…] mitogenomes based on the two methods were aligned and manually checked for consistency. to check read support consistency, reads were mapped to final assembled mitogenomes and visualized using integrated genome viewer., mitogenome annotation was done using mitos2 that includes the latest protein identification model,. we used two references in mitos2, refseq63 metazoa and refseq81 metazoa, […]

library_books

Mutation analysis of BRCA1/2 mutations with special reference to polymorphic SNPs in Indian breast cancer patients

2018
PMCID: 5953318
PMID: 29785135
DOI: 10.2147/TACG.S155955

[…] scientific), which identified nonsynonymous mutations. splice site alteration were analyzed 2 bp upstream or downstream of exon–intron boundaries. sequence data were visually confirmed with the integrative genomics viewer (igv) and any sequence, alignment, or variant call error artifacts were discarded. nonsynonymous mutations were annotated using the breast cancer information core (bic) […]


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IGV institution(s)
School of Medicine, University of California San Diego, La Jolla, CA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Pacific Biosciences, Menlo Park, CA, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
IGV funding source(s)
Supported by the NCI (NIH/NCI) grants R01CA157304 and U24CA210004 and the Starr Cancer Consortium grant I5-A500.

IGV reviews

 (2)
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Gyan Prakash Mishra

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Desktop
IGV is the first choice for quick visualisation of NGS data. It takes BAM file (along with .bai file), .bedGraph file, .bigWig.

Fabien Pichon

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Desktop
A simple viewer. You can not do a lot with it, but you can visualize your mapping and that's its job !
To me, it miss however the possibility to add landmarks (vertical lines).