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A: http://www.sph.umich.edu/csg/yli/mach/download/ <br>
A: http://www.sph.umich.edu/csg/yli/mach/download/ <br>
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=== '''Does --mle overwrite fed-in genotypes?''' ===
=== '''Does --mle overwrite fed-in genotypes?''' ===
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=== '''Shall I apply QC before or after imputation? If so, how? ''' ===
=== '''Shall I apply QC before or after imputation? If so, how? ''' ===
A: Yes. 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%.
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=== '''How do I get reference files for an region of interest? ''' ===
=== '''How do I get reference files for an region of interest? ''' ===
awk '{print $3}' orig.hap | cut -c${first}-${last} > region.hap
awk '{print $3}' orig.hap | cut -c${first}-${last} > region.hap
=== '''Do I have to sort the pedigree file by physical positions? ''' ===
=== '''Do I have to sort the pedigree file by physical positions? ''' ===
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=== '''How is AL1 defined? Which allele dosage is .dose/.mldose counting?''' ===
=== '''How is AL1 defined? Which allele dosage is .dose/.mldose counting?''' ===
A: AL1 is an arbitrary allele. To be specific, it is the first allele read in the reference haplotypes (file fed to -h or --haps). The earliest versions of mach1 counted the number of AL2 and the latest versions count the number of AL1. One can find out which allele is counted following the steps below. <br>
> head -2 mlinfo/chr21.mlinfo
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:
of AL1 copies: you will only to check for one informative case (i.e,
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> head -1 mldose/chr21.mldose | cut -f3 -d ' ' 1.962 > head -2 mlinfo/chr21.mlinfo SNP Al1 Al2 Freq1 MAF Quality Rsq rs885550 2 4 0.9840 0.0160 0.9682 0.0021 head -1 mlgeno/chr21.mlgeno | cut -f3 -d ' ' 2/2
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Based on the three files above, we've confirmed that dosage is the number of AL1 copies: you will only to check for one informative case (i.e, dosage values close to 0 or 2) since it's consistent across all individuals and all SNPs.
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=== '''Can I used unphased reference?''' ===
=== '''Can I used unphased reference?''' ===
