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RAREMETALWORKER command reference

565 bytes added, 12:07, 19 June 2014
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.
 
==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==
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