From: Impact of pre-imputation SNP-filtering on genotype imputation results
Datasets | MaCH Imputation score observing 10% overlapping masked SNPs | IMPUTE2 Imputation score observing 10% overlapping masked SNPs | |||||
---|---|---|---|---|---|---|---|
Data subset name | #SNPs | 10% | 20% | 50% | 10% | 20% | 50% |
ALL | 9602 | 98.29 | 98.72+ | 98.07+ | 99.57+ | 99.57+ | 99.36 |
LQ | 8472 | 98.29 | 98.50 | 98.07 | 99.57 | 99.57 | 99.57+ |
NQ | 7923 | 98.50+ | 98.50 | 97.64 | 99.57 | 99.57 | 99.36 |
BQ | 6337 | 96.57 | 96.57 | 92.72 | 99.14 | 98.93 | 97.43 |
HQ | 4658 | 96.36 | 96.36 | 91.65 | 98.50 | 98.07 | 96.36 |