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MaCH FAQ

4 bytes added, 20:13, 28 November 2010
Why and how to perform a 2-step imputation?
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
In step1, one can use --greedy in combination with --states XX in MaCH versions 16.b and above. We have found that using 1/3 of the reference haplotypes (with 1/9 computational time) results in almost no power loss for the current HapMap and 1000G reference panels.<br>
In step2, each individual is imputed independently and can therefore be split into as many as n (sample size) jobs for each chromosome for parallelism.
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