Pre-phasing for imputation BEAGLE or MACH

Question

[Laura]

Hello,

I'm performing pre-phasing for imputation in MACH. However, this is very time consuming. There are 950 individuals and for chromosome 4, there are ~37.000 SNPs, for example.

I've read that BEAGLE is faster but less accurate depending on sample and marker size. In this case, do you think using BEAGLE would be a problem?

Answer 1

[nchuang]

Check out SHAPEIT.