Statistical Model For Genotyping Based On Putative Structural Variants

Question

[michealsmith]

Suppose now I've identified putative structural variants (for example deletion) based on discordant read pair and split-read approach. And I would like to further look at the read-depth information within these callings, for both additional supporting evidences (for example, I would toss out the putative callings if read density is quite high within candidate callings of deletion), and genotyping (to know it's heterozygous or homozygous deletion).

I know basically we need to calculate the normalized average read depths within the candidate callings. But I'm wondering what model/statistics I could use? Say, Gaussian mixture model? Any other ideas?

Thanks

Answer 1

[zam.iqbal.genome]

I think this paper by Bob Handsaker should help:

http://www.nature.com/ng/journal/v43/n3/full/ng.768.html

best

Zam