Question: Statistical Model For Genotyping Based On Putative Structural Variants
gravatar for michealsmith
7.1 years ago by
michealsmith740 wrote:

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?


sv genotyping • 1.2k views
ADD COMMENTlink written 7.1 years ago by michealsmith740
gravatar for zam.iqbal.genome
7.0 years ago by
United Kingdom
zam.iqbal.genome1.7k wrote:

I think this paper by Bob Handsaker should help:



ADD COMMENTlink written 7.0 years ago by zam.iqbal.genome1.7k
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