I am using the lowresbam2raster and successfully generated the CNV graphs. I have a question on the depth panel. Here are the two graphs generated:
Both of them are from the same region, and the second sample was identified to have a deletion here by LUMPY and DELLY (the CNV calling softwares) with SR (supportive reads) value equal to 10 (WGS converage is 30X). But I didn't see an obvious coverage drop of the depth in the second graph when compared to the depth of the first graph (without deletion in the region).
My question is: If there must be an obvious coverage drop in the depth panel so the deletion can be considered as true positive?
Hi @lindenb ,
I am using the lowresbam2raster and successfully generated the CNV graphs. I have a question on the depth panel. Here are the two graphs generated:
Both of them are from the same region, and the second sample was identified to have a deletion here by LUMPY and DELLY (the CNV calling softwares) with SR (supportive reads) value equal to 10 (WGS converage is 30X). But I didn't see an obvious coverage drop of the depth in the second graph when compared to the depth of the first graph (without deletion in the region).
My question is: If there must be an obvious coverage drop in the depth panel so the deletion can be considered as true positive?
thanks,
Shan