Displayed Read Depth Question

[erik zmuda]

Hi!

I'm trying to account for total depth of reads shown when clicking on the coverage track as positions where insertions are anchored. Can you confirm that the number of reads shown for insertions is already included in the total? It is a little confusing that reference at these positions seems to contribute to the total depth, but we have additional reads attributed to the insertion. We were thinking we needed to add the reads from insertion to the total when trying to manually calculate VAF for the insertion (ie. VAF= Ins read #/(total reads+ins read#). 

This may be flawed approach given that the adjacent positions, which we would expect to have similar depth of coverage, do not have a jump in read depth that mirrors the '"total reads+ins read#".

Just wondering if you can confirm that total depth already accounts for the reads attributed to the insertion?

[igv-help]

I'm not sure I'm following the question.   The total count is just the count of reads overlapping the given position.   Insertions per se do not have a reference position, by definition, they are between reference positions.    For purposes of the INS count in the popup text,  the count should appear at the reference position just before the insertion.

I don't understand what you mean by "reads attributed to the insertion".