What is it?
snps_mincounts the number of sites in a given imputation reference panel that is covered by at least one read in the sample being analyzed and fails if it is smaller than some specified minimum (typically corresponding to ~10% of polymorphic sites in the reference panel)
effective_coverage_minis a function of the number of sites covered by at least one read and a given reference panel. A more detailed description can be found in the “Defining effective coverage” section of the paper linked here.
- Since imputation relies on the presence of data across the genome, failing this step indicates that there is insufficiently even coverage across the genome for reliable analysis
Possible reasons for failure:
- Insufficiently evenly distributed sequence coverage across the genome
- Uneven coverage is typically due to factors involved upstream of data generation such as library preparation.