-pedfile <filename>

Specify a genotype input file (or http:// location) in pedigree
format. This option works in GUI mode.

-hapmap <filename>

Specify a HapMap
format input file (or http:// location). This option works in GUI mode.

-phasedhmpdata <filename>

Specify a PHASE
format data input file (or http:// location). This option works in GUI mode.

-phasedhmpsample <filename>

Specify a PHASE
format sample input file (or http:// location). This option works in GUI mode.

-phasedhmplegend <filename>

Specify a PHASE
format legend input file (or http:// location). This option works in GUI mode.

-hapmapDownload

Specify a phased HapMap download. This option works in GUI mode.

-haps <filename>

Specify a phased input file (or http:// location). This option works in GUI mode.

-info <filename>

Specify a marker information file (or http:// location). This option works in GUI mode.

-plink <filename>

Specify a PLINK or other results file (or http:// location). This option only works in GUI mode.

-map <filename>

Specify a map or binary map file (or http:// location). This option only works in GUI mode.

-batch <filename>

Specify a batch load file.

-blocks <filename>

Specify a block definition file (or http:// location). This will automatically use this block definition for haplotype output.

-track <filename>

Specify an analysis track file (or http:// location)

-chromosome <1-22,X,Y>

Specify
which chromosome these data come from. This is especially critical when
analyzing data from the X chromosome or direct HapMap downloads.

-panel <CEU,YRI,CHB+JPT>

Specify which analysis panel to use for phased HapMap downloads.

-startpos <integer (in kb)>

Specify the start position in kb for phased HapMap downloads.

-endpos <integer (in kb)>

Specify the end position in kb for phased HapMap downloads.

-release <16a,21,22>

Specify the HapMap release version for phased HapMap downloads (defaults to 21).

-gzip

Specify PHASE format inputs using GZIP compression

-nonSNP

Specify that the accompanying PLINK file is non-SNP based output. This option only works in GUI mode.

-selectCols

Activate the preloading column filter for PLINK loads. This option only works in GUI mode.