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# 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
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=== '''Where can I find combined HapMap reference files? ''' ===
=== '''Where can I find combined HapMap reference files? ''' ===
We strongly recommend QC both before and after imputation. Before imputation, we recommend the standard battery of QC filters including HWE, MAF (recommended cutoff is 1% for genotyping-based GWAS), completeness, Mendelian inconsistency etc. Post-imputation, we recommend Rsq 0.3 (which removes >70% of poorly-imputed SNPs at the cost of <0.5% well-imputed SNPs) and MAF of 1%.
We strongly recommend QC both before and after imputation. Before imputation, we recommend the standard battery of QC filters including HWE, MAF (recommended cutoff is 1% for genotyping-based GWAS), completeness, Mendelian inconsistency etc. Post-imputation, we recommend Rsq 0.3 (which removes >70% of poorly-imputed SNPs at the cost of <0.5% well-imputed SNPs) and MAF of 1%.
=== '''How do I get reference files for an region of interest? ''' ===
=== '''How do I get reference files for an region of interest? ''' ===
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=== '''What if I specified --states R where R exceeds the maximum possible (2*number diploid individuals - 2 + number_haplotypes)? ''' ===
=== '''What if I specified ''--states R'' where ''R'' exceeds the maximum possible (2*number diploid individuals - 2 + number_haplotypes)? ''' ===
Mach will automatically change this to the maximum possible value.
Mach will automatically change this to the maximum possible value.
=== '''How is AL1 defined? Which allele dosage is .dose/.mldose counting?''' ===
=== '''How is AL1 defined? Which allele dosage is .dose/.mldose counting?''' ===
