Phase 3 (analyse significance)

Required Positional Arguments: [1] Working Directory SelecT working directory created in Phase 1. Working Directory name can be changed but subdirectory names must be unchanged.

[2] Chromosome Chromosome number where window can be found

Optional Arguments: -co Combine Only Only runs first half of analysis where windows are combined into one file.

--combine_fltr Combine Filter Uses a specific filter for printing specific combination of stats in output. Can only be used in conjunction with the -co flag i=iHS, x=XPEHH, h=iHH, dd=dDAF, d=DAF, f=Fst, up=unstd_PoP, um=unstd_MoP, p=PoP, m=MoP. Each tag should be separated by a colon (i.e. i:x:h:dd:d:f:up:um:p:m).

--p_value p_Value Sets the p-value cutoff for significance check on composite scores. Defaults to 0.01

-wc Write Combine Similar to -co, but also runs significance filtering

-rn Normalization Runs normalization step across the entire dataset/chromosome. Normalizes by standardization (mean 0; standard deviation 1).

-ui Use Incomplete Use incomplete data when analyzing MoP scores

-im Ignore MoP Ignores all MoP scores and finds significance based upon PoP only.

-ip Ignore PoP Ignores all PoP scores and finds significance based upon MoP only. If both -im and -ip flags are present significance is found by looking at either PoP or MoP. If neither -im or -ip flag is present significance is found by looking at both PoP and MoP.

Examples: java -Xmx[MB]m -jar SignificanceAnalyzer.jar [1] [2] java -jar SignificanceAnalyzer.jar example/SelecT_workspace 21