Input Options
-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.