CNV and Depth of coverage statistical method
Hi,
I have depth of coverage file generated by GATK having depth of coverage for 20 samples on each chromosome. I am interested in comparison between samples using some statistical method to find structural variants like deletions.
I started by normalizing the read depth as it is different for different samples.Is there anyone who could suggest me some method to normalize and apply statistical method to see these marks?
So far what I have done this for one of chromosome:
1.calculated depth in 100 bp window for each sample (by simple taking sum)
2.calculate z-score of sums for each sample.
what next?? Should i check fold change? How?
Is this the right way to start with?
Any script, or suggestion will work. ()
I have depth of coverage file generated by GATK having depth of coverage for 20 samples on each chromosome. I am interested in comparison between samples using some statistical method to find structural variants like deletions.
I started by normalizing the read depth as it is different for different samples.Is there anyone who could suggest me some method to normalize and apply statistical method to see these marks?
So far what I have done this for one of chromosome:
1.calculated depth in 100 bp window for each sample (by simple taking sum)
2.calculate z-score of sums for each sample.
what next?? Should i check fold change? How?
Is this the right way to start with?
Any script, or suggestion will work. ()