Phase 1 (environmental setup)

#####Required Positional Arguments:

[1] Data Directory Directory should contain all phased VCF or HAP/LEGEND file required for selection analysis. File names must contain proper flags and file extensions. Include optional (but highly recommended) Ancestral data embedded in VCF files or as separate LEGEND/EMF file

[2] Map Directory Directory that contains all required genetic map files for SelecT analysis. File names must contain proper chromosome flags.

[3] Start Chromosome Must be a number between 1-22; sex chromosomes not yet supported.

[4] End Chromosome Must be a number between 1-22 and greater or equal to Start Chromosome; sex chromosomes not yet supported.

[5] Target Population Population identifier for experimental population TST can be used if no standard indentifier exists

[6] Cross Population Population identifier for cross population TST can be used if no standard indentifier exists. Cross Population cannont be the same as Target Population.

#####Optional Arguments: --out_pop Outgroup Population Population identifier for outgroup population. TST can be used if no standard indentifier exists. Outgroup Population cannont be the same as Target Population.

--working_dir Working Directory Defines the directory where SelecT will create a new working directory. Default is current directory.

--win_size Window Size For changing SelecT analysis window size (in megabases. Default is 0.5Mb.

Examples: java -Xmx[MB]m -jar EnviSetup.jar [1] [2] [3] [4] [5] [6]
--working_dir=path/to/directory java -Xmx3000m -jar EnviSetup.jar example/haplegend_data example/map 21 21 CEU YRI
--working_dir=example