Impute specific variants using QUILT

[biozzq]

Hi,

Since my focus is on specific regions and variants on the genome, I'm wondering if I can remove non-targeted positions from the reference panel before imputation to reduce the running time. However, I'm concerned about whether this would significantly affect the accuracy of the imputation.

Additionally, I'm trying to determine the best approach for using QUILT with a window size of 2Mb. Would running QUILT by sample produce higher imputation accuracy, or should I run QUILT with all samples together? I'd appreciate any insights on which strategy is more effective.

Best wishes, Zheng zhuqing