What is it?
- This QC checks that the average “call confidence” (CC) genome-wide is above some threshold.
- CC is defined at in section 2.4 of the linked paper, and is a phred-scaled measure of genome-wide imputation quality.
Possible reasons for failure:
- Low average imputation quality due to a number of possible reasons, including the possibility that the population to which the sample being processed belongs is not well-represented in the imputation reference panel.