What is the well-recognized standard of coverage uniformity
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3 months ago
CY ▴ 610

We are working on a project of developing CNV caller. We believe that efficacy of hybrid probe (targeted sequencing) is one of the factor that may affect degree of bias of depth. We therefore would like to check if the coverage uniformity of our samples is within acceptable range. My question is what is the well-recognized standard of coverage uniformity?

Also, my instinction is that, theoretically, CNV calling requires more stringent criteria of coverage univormity than SNV calling since it is more vulnerable to bias of depth. Does my impression make sense?

sequencing CNV depth uniformity coverage • 232 views
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Hi, a typical measure of coverage variability would be a signal-to-noise ratio.

CNV calling requires more stringent criteria of coverage univormity than SNV calling since it is more vulnerable to bias of depth

It is really dependent on which CNVs one wants to detect. Large CNVs calling can be performed in e.g. 0.5x WGS while SNVs calling obviously not.

Good luck with the development!