1,555
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Why and how to perform a 2-step imputation?
=== '''Why and how to perform a 2-step imputation?''' ===
=== '''Why and how to perform a 2-step imputation?''' ===
When one has a large number of individuals (>1000), we recommend a 2-step imputation to speed up. <br>
A 2-step imputation contains the following 2 steps:<br>
A 2-step imputation contains the following 2 steps:<br>
Example command lines for a 2-step imputation:<br>
Example command lines for a 2-step imputation:<br>
#step 1:
# step 1:
mach1 -d sample.dat -p subset.ped -s chr20.snps -h chr20.hap --compact --greedy --autoFlip -r 100 -o par_infer > mach.infer.log
mach1 -d sample.dat -p subset.ped -s chr20.snps -h chr20.hap --compact --greedy --autoFlip -r 100 -o par_infer > mach.infer.log
# step 2:
# step 2:
mach1 -d sample.dat -p sample.ped -s chr20.snps -h chr20.hap --compact --greedy --autoFlip --errorMap par_infer.erate --crossoverMap par_infer.rec --mle --mldetails > mach.imp.log
mach1 -d sample.dat -p sample.ped -s chr20.snps -h chr20.hap --compact --greedy --autoFlip --errorMap par_infer.erate --crossoverMap par_infer.rec --mle --mldetails > mach.imp.log
=== '''Where can I find combined HapMap reference files? ''' ===
=== '''Where can I find combined HapMap reference files? ''' ===
