I am working with samples with different levels of coverage from publically available data. Some samples have 50x and they have same PSMC plot, as they should. However some samples from the same population, have the same pattern but around a third of the numbers of Ne and I think is due to low coverage. The samples with lower coverage range from 7-14x. Do you have a recommendation on how to calculate the the fraction of hets missed due to low coverage?
Thank you!
I am working with samples with different levels of coverage from publically available data. Some samples have 50x and they have same PSMC plot, as they should. However some samples from the same population, have the same pattern but around a third of the numbers of Ne and I think is due to low coverage. The samples with lower coverage range from 7-14x. Do you have a recommendation on how to calculate the the fraction of hets missed due to low coverage?
Thank you!