Hi everyone, I'd really apreciate some advice on the analylisis I'm trying to do. I have a genomewide data for allele frequency for my population of interest and I'm comparing these to frequencies from european population. Overall its very similar but at some sites I can see clear differences:
overall plot of B allele frequencies, between my population and European population
zoomed in fragment:
I supose, that I can call CNV sites from such picture. It is quite the same as a MAF plots for cancer tissue used in many packages for such analysis (GATK for example https://gatk.broadinstitute.org/hc/en-us/articles/360035890011)
But I failed to find any software that does it (basically calls a segments from my plot)? Are these tasks fundamentally different and I'm missing something here? Is it so trivial that no one bother to do so and just implements some sliding window approaches? Is it a rare task? Do I need some other starting data? (for my population I obviously have a full set, but for European population from gnomad I can only have some summary statistics..
Best, Eugene
