ITCR grant: The Integrative Genomics Viewer (IGV ...IGV_ITCRPImtg_April2017.pdfIntegrative Genomics...
Transcript of ITCR grant: The Integrative Genomics Viewer (IGV ...IGV_ITCRPImtg_April2017.pdfIntegrative Genomics...
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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