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, 12:07, 19 June 2014
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| * --xStart takes an integer that described the end position of nonPAR region on chromosome X. | | * --xStart takes an integer that described the end position of nonPAR region on chromosome X. |
| * The default is 154931044 based on Human Genome build 19. | | * The default is 154931044 based on Human Genome build 19. |
| + | |
| + | ==Others== |
| + | ===--cpu[1]=== |
| + | *--cpu takes an integer that specifies the number of cpus to use for estimating kinship matrix from genotypes. |
| + | |
| + | ===--kinOnly=== |
| + | *--kinOnly allows users to estimate kinship matrix without any association analysis of any traits included in the data set. |
| + | *To also estimate chromosome X kinship, --vcX option should be added in command line. |
| + | |
| + | ===--geneMap=== |
| + | * --geneMap takes a string describing the path to find mapping file for manhattan plot annotation. |
| + | * The default is human genome build 19, saved in raremetal/data/refFlat_hg19.txt. |
| | | |
| ==PhoneHome== | | ==PhoneHome== |