ITCRgrant:TheIntegrativeGenomicsViewer(IGV):VisualizationSupportingCancerResearchPI:JillP.Mesirov,UCSanDiego

CollaborativeSet-AsideProjectwithKarchin Lab,JohnsHopkinsUniversity

ITCRPIMeeting,April72017HelgaThorvaldsdottir

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IntegrativeGenomicsViewer(IGV)

>Providesvisualexplorationofgenomicdata.

>Frequentlyusedforvisualinspectionofdataunderlyingputativevariantscalledbycomputationalmethods.

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IntegrativeGenomicsViewer(IGV)

Goalofourcollaborativeset-asideproject:ProvideIGVuserswithtoolstohelpassessthefunctionalsignificanceofsomaticmutationsandgermlinepolymorphismstheyviewinIGV.

>Providesvisualexplorationofdataproducedbygenomicstudies.

>Frequentlyusedforvisualinspectionofdataunderlyingputativevariantscalledbycomputationalmethods.

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Cancer-relatedAnnotationofVariantsToolkit(CRAVAT)

MutationPositionImagingToolkit(MuPIT)

Providespredictivescoresforgermlinevariants,somaticmutationsandrelativegeneimportance,aswellasannotationsfrompublishedliteratureanddatabases.

MapsSNVsfromgenomiccoordinatesontoproteinstructuresandprovidesaninteractivevisualizationtool.

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DirectlinksfromIGVtoCRAVAT

1. ClickonavariantinIGVtrack(.bam,.vcf,.maf tracks)à OpenwindowwithCRAVAT annotations

2. ClickonavariantinIGV track(.bam,.vcf,.maf tracks)à LaunchCRAVAT analysis

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DirectlinksfromIGVtoCRAVAT

1. ClickonavariantinIGVtrack(.bam,.vcf,.maf tracks)à OpenwindowwithCRAVAT annotations

2. ClickonavariantinIGV track(.bam,.vcf,.maf tracks)à LaunchCRAVAT analysis

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DirectlinksfromIGVtoCRAVAT

UserentersCRAVATanalysisoptions

1. ClickonavariantinIGVtrack(.bam,.vcf,.maf tracks)à OpenwindowwithCRAVAT annotations

2. ClickonavariantinIGV track(.bam,.vcf,.maf tracks)à LaunchCRAVAT analysis

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DirectlinksfromIGVtoCRAVAT

1. ClickonavariantinIGVtrack(.bam,.vcf,.maf tracks)à OpenwindowwithCRAVAT annotations

2. ClickonavariantinIGV track(.bam,.vcf,.maf tracks)à LaunchCRAVAT analysis

UserentersCRAVATanalysisoptions

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DirectlinksfromIGVtoMuPIT

1. Clickonavariant inIGVtrack(.bam,.vcf,.maf tracks)à Viewvariant inMuPIT 3Dproteinstructureviewer

2. Clickanywhere inanyIGVdatatrackà Viewlocus inMuPIT 3Dproteinstructureviewer

3. Clickonexon inIGVgeneannotationtrackà Viewgene inMuPIT 3Dproteinstructureviewer

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DirectlinksfromIGVtoMuPIT

1. Clickonavariant inIGVtrack(.bam,.vcf,.maf tracks)à Viewvariant inMuPIT 3Dproteinstructureviewer

2. Clickanywhere inanyIGVtrackà Viewlocus inMuPIT 3Dproteinstructureviewer

3. Clickonexon inIGVgeneannotationtrackà Viewgene inMuPIT 3Dproteinstructureviewer

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DirectlinksfromIGVtoMuPIT

1. Clickonavariant inIGVtrack(.bam,.vcf,.maf tracks)à Viewvariant inMuPIT 3Dproteinstructureviewer

2. Clickanywhere inanyIGVtrackà Viewlocus inMuPIT 3Dproteinstructureviewer

3. Clickonexon inIGVgeneannotationtrackà Viewgene inMuPIT 3Dproteinstructureviewer

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IGVDesktopand igv.js

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