Coverage Diff Between Case And Control Exome Data

Question

[ewre]

Hi,all I have used public avialable exome data as control in my analysis. due to different enrichment platforms used between case(agilent V4) and control(nimblegen seqcap v2) , I have observed more snvs(variant calling using the intersection part of the two platforms mentioned above) in controls compared with cases. what i wander is that are there any additional procedure I should do to remove the bias due to the enrichment platform diiferences?

Answer 1

[DG]

In general, and I'm not an expert on this, but for most procedures for looking for possible SNVs from exome data mixing platforms is typically not a good idea and there are some random aspects you probably won't be able to control for very well. One thing you can do is compare your targeted regions between the capture kits. Any regions that don't overlap significantly in terms of targeted capture you know immediately you have no reliable information on.

[ewre]

thanks for the suggestion. I used the common part of capture kits to do variant calling. well, more variants are called from control than case. I guess the difference of sequencing depth and coverage between case and ctrl may have a influence. i wander if there are methods i can take to do an adjustment.