Question: Pre-phasing for imputation BEAGLE or MACH
0
gravatar for Laura
4.3 years ago by
Laura20
UFRGS, Brazil
Laura20 wrote:

Hello,

I'm performing pre-phasing for imputation in MACH. However, this is very time consuming. There are 950 individuals and for chromossome 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?  

 

ADD COMMENTlink modified 4.3 years ago by nchuang210 • written 4.3 years ago by Laura20
2
gravatar for nchuang
4.3 years ago by
nchuang210
United States
nchuang210 wrote:

check out SHAPEIT 

https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#prephasing

ADD COMMENTlink written 4.3 years ago by nchuang210
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