RC calculation

[David F]

Good morning Tobias,

First I wanted to thank you for diligently answering questions on this form. As a user of the tool I really appreciate it.

In my sample delly calls a deletion on chr1: 82,660,275 - 82,661,887 (1612bp). It is a heterogeneous precise variant with an RC = 30, RCL = 82, & RCR = 81.

The delly vcf says "Raw high-quality read counts or base counts for the SV." How is RC calculated? Does that mean those individual reads within the start and end points? If I wanted to manually calculate this number for my variant how would I do this. Basically, I am looking to understand how RC is calculated what it really means for any given call.

Thanks very much for your time and assistance.

[Tobias Rausch]

Hi,

RC is the coverage inside the SV and RCL and RCR the values to the Left and Right. The copy-number estimate is then simply  2 * RC / (RCL+RCR) because RCL and RCR are half the size of the SV (assuming diploidy).

https://github.com/dellytools/delly/blob/main/src/modvcf.h?plain=1#L536

Best, Tobias

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