IGV Hands-on Exercise Viewing variants (VCF file)
Transcript of IGV Hands-on Exercise Viewing variants (VCF file)
1.Loaddata
ClickFile>OpenSession
Genotypes
Thennavigatetotheworkshopfolder /igvData /vcfandopenvcf_session.xml
2.Observethedifferentdatapanels
Variantsites
Sampleinformation
Hoveroverthevariantsitesandthegenotypestoseethedetails.(Ifyouchangedthepopupbehaviorwiththetool,youmayhavetoclick toseethedetails)
Observe howthesamevaluesinthesampleinformationpanelareassignedthesamecolor.Tryclickingonthesampleinformationcolumnheaderstosortbyattribute.
Sampleinfocolumnheaders
3.HighlightinterestingeventingeneAPOL1
- TypeAPOL1:S342GinthesearchboxandclickGo
- Right-clickovergenotypesandselectDisplayMode:Squished
Viewingvariants(VCFfile)-page1
IGVHands-onExercise Viewingvariants(VCFfile)
4.ObservedifferencesbetweengroupsUsethescrollbartoscrolldownandseeallthegroups.
Notethatthevariantsatthislocusarenotpresentinsomepopulationgroupsandprevalentinothers.
Scrollbar
3.(continued)HighlightinterestingeventingeneAPOL1
- Right-clickovergenotypesandselectGroupBy,thenselectattributesuper_pop.
Viewingvariants(VCFfile)-page2
ENDOFEXERCISE