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#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? ''' ===
Take your dosage, geno, and info output (.dose, .geno and .info or .mldose, .mlgeno, and .mlinfo depending on non-mle or mle manner you've used) and check if dosage is the number of AL1 copies or AL2 copies. Example is given below:
Take your dosage, geno, and info output (.dose, .geno and .info or .mldose, .mlgeno, and .mlinfo depending on non-mle or mle manner you've used) and check if dosage is the number of AL1 copies or AL2 copies. Example is given below:
<br>
head -1 mldose/chr21.mldose | cut -f3 -d ' '
'''head -1 mldose/chr21.mldose | cut -f3 -d ' ' '''
1.962
1.962
'''head -2 mlinfo/chr21.mlinfo '''
SNP Al1 Al2 Freq1 MAF Quality Rsq
SNP Al1 Al2 Freq1 MAF Quality Rsq
rs885550 2 4 0.9840 0.0160 0.9682 0.0021
rs885550 2 4 0.9840 0.0160 0.9682 0.0021
''' head -1 mlgeno/chr21.mlgeno | cut -f3 -d ' ' '''
2/2
2/2
