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=== '''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>
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:
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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.
=== '''Can I used unphased reference?''' ===
=== '''Can I used unphased reference?''' ===
