Table 1 Overview of sQC
From: Look who is calling: a comparison of genotype calling algorithms
No. SNPs removed (%) | |||
|---|---|---|---|
QC criteria | BRLMM | Chiamo++ | JAPL |
Failed MAF | 37,259 (8.85%) | 44,181 (10.45%) | 39,201 (9.27%) |
Failed MiF | 76,528 (18.11%) | 41,939 (9.92%) | 62,969 (14.90%) |
Failed HWE | 7,519 (1.78%) | 16,891 (4.00%) | 7,208 (1.71%) |
Passed all sQC | 312,982 (74.05%) | 326,950 (77.36%) | 320,707 (75.88%) |