From Genome Analysis Wiki
→How is AL1 defined? Which allele dosage is .dose/.mldose counting?
== How is AL1 defined? Which allele dosage is .dose/.mldose counting? ==
AL1 is an arbitrary allele. Typically, it is the first allele read in the reference haplotypes
(file fed to -h or --haps). The earliest versions (prior to April 2007) of mach counted the expected number copies of AL2 and more recent versions count the number of AL1. One can find out which allele is counted following the steps below.
#. First, find the two alleles for one of the markers in your data
Note that, on the example above, .mldose could be replaced with .dose and .mlgeno could be replaced with .geno.
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 an unphased reference? ==