#!/bin/sh


# pre-phase with mach 
./mach1 -d sample.dat -p sample.ped --rounds 20 --states 50 --phase --prefix sample.pp | tee mach.log


# impute with minimac
./minimac --refHaps hapmap.hap --refSnps hapmap.snps --haps sample.pp.gz --snps sample.snps --prefix sample.imp | tee minimac.log

