Recall genotypes from Illumina idat files using crlmm package
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nadne ▴ 10
@nadne-9806
Last seen 5.2 years ago

Hello,

I want to get the genotype recall from idat files. I have few thousands samples, and I'm not sure how to do that efficiently. I used the next set of commands:

library(crlmm)
library(ff)
library(snow)
library(doSNOW)
cl <- makeCluster(90, type="SOCK")
registerDoSNOW(cl)
options("krlmm.cores" = 90)
ocProbesets(150e3)
ocSamples(5000)
dir_name = ‘set1’ # Directory contains 500 samples
g = genotype.Illumina(cdfName='humanomni25quadv1b', path=dir_name, call.method='krlmm', verbose=TRUE)

Can someone please help me in fine tuning the different parameters: 

ocProbesets, ocSamples, krlmm.cores, snow, ff

Are all needed or are they masking each-other?

Can someone give me rough estimation of runtime? Should I expect hours, days or weeks?

I have access to different machine with up to 100 cpus and up to 1T RAM, how can I take advantage of such?

crlmm genotype • 997 views
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