BEAGLE is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. You must provide the genotypes in the formats described in their documentation here in PDF. An annotation file containing the marker info has to be provided as well.

Sample affection info may be delivered in beagles genotype file, but you can make use of GWASpi’s Sample Info & Phenotype file function to provide more information on your Samples.

Example of a Beagle genotype file:
I id 1008 1008 1040 1040 1179 1179 1183 1183
A affection 1 1 1 1 2 2 2 2
M rs9560418 A A G A G A G G
M rs7325963 C C A C A C A A
M rs7325274 T T C T C T C C
M rs7326018 T T A T A T A A
M rs9515606 T T A T A T A A
M rs9560419 C C A C A C A A
M rs9522650 G G A G A G A A
M rs4386004 A A G A G A G G
M rs9515608 T T C T C T C C
M rs1409911 T T C T C T C C
M rs7320791 G G C G C G C C
M rs7320801 T T C T C T C C
Example of a Beagle annotation or marker mapping file:
rs9560418 89162302 A G
rs7325963 89163844 A C
rs7325274 89163886 C T
rs7326018 89163923 A T
rs9515606 89163953 A T
rs9560419 89164148 A C
rs9522650 89164321 A G
rs4386004 89164848 A G
rs9515608 89164920 C T
rs1409911 89165586 C T
rs7320791 89166331 C G
rs7320801 89166351 C T