Input and output

--bfile test
Input PLINK binary PED files, e.g. test.fam, test.bim and test.bed (see PLINK user manual for details).

--dosage-mach test.mldose test.mlinfo
Input files in MACH output format (uncompressed), e.g. test.mldose and test.mlinfo (see MACH user manual for details).
--dosage-mach-gz test.mldose.gz test.mlinfo.gz
Input files in MACH output format (compressed), e.g. test.mldose.gz and test.mlinfo.gz.

Formats of the input files
test.mldose
001->0011 ML_DOSE 2.000 0.000 0.000 0.000 2.000 0.001 0.028 0.017 1.992 0.027
002->0021 ML_DOSE 2.000 1.000 1.000 1.000 1.999 1.001 1.280 1.010 1.985 1.028
003->0031-000 ML_DOSE 1.036 1.132 1.000 2.000 1.003 1.999 0.986 1.013 1.030 1.984
...

test.mlinfo
SNP Al1 Al2 Freq1 MAF Quality Rsq
rs1 G T 0.8633 0.1367 0.9595 0.8697
rs2 C T 0.4654 0.4654 0.9702 0.9543
rs3 G T 0.4459 0.4459 0.9997 0.9995
...

Note: the --dosage-mach option was designed to read output files from an early version of MACH, which might not be compatible with output files from the latest version of MACH or Minimac.

--out test
Specify output root filename.