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