From: Impact of pre-imputation SNP-filtering on genotype imputation results
Datasets | MACH Imputation score based on 10% overlapping masked genotypes | IMPUTE2 Imputation score based on 10% overlapping masked genotypes | |||||
---|---|---|---|---|---|---|---|
Data subset name | #SNPs | 10% | 20% | 50% | 10% | 20% | 50% |
ALL | 9602 | 94.03*+ | 93.44* | 91.03*+ | 93.12+ | 92.42+ | 89.74 |
LQ | 8472 | 94.01* | 93.45*+ | 91.01* | 93.10 | 92.41 | 89.85+ |
NQ | 7923 | 93.83* | 93.15* | 90.61* | 92.90 | 92.11 | 89.32 |
BQ | 6337 | 90.85* | 89.62* | 83.34* | 89.85 | 88.61 | 82.47 |
HQ | 4658 | 90.47* | 89.05* | 81.84* | 89.00 | 87.55 | 80.57 |