1******************** Command line options ****************
| Required parameters | Description |
|---|---|
| -d, –ped <File> | ped file name |
| -o, –operation, –program <Integer> | analysis to run: 1..4 {Pvalue(default), Threshold, MultiAssess, CaseControl} |
| -p, –ld, –par <File> | par or ld file |
| Optional parameters | Description |
|---|---|
| –accumulator | hostname:port of accumulation service |
| –confidence [Integer] | Confidence level for p-value bounds:1=95%;2=99%;3=99.9 (default: 1) |
| –dbname | project/PI specific database name |
| –effortName | unifiying name for related, accumulated SGSPValue runs |
| -f, –report <File> | primary output file (or dir) |
| -h, –help | |
| –maxtime [Integer] | Maximum running time in seconds (default 25800:3 days less 20 minutes) |
| -n, –simscount [Long] | number of simulations (default: 1000) |
| –segmentsFile <File> | file of segments as lines from .pval |
| –simFile <File> | name of file for simulated genotypes |
| –simPval | use first simulated gt set as ‘observed’, get pval |
| –skipLength [Integer] | minimum size of analyzable segment (default: 20) |
| –threshold <Float> | Genome-wide threshold against which we compare p-values at run-time |
| –trim | Set of probands by which to trim pedigree, filename or comma separated ids |
Subset of probands to which to trim extraneous members from the pedigree. If not used, all individuals marked as affected in the PED file will be assessed. However, the pedigree is still trimmed to this exhaustive set.