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Revision as of 13:09, 14 April 2014
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==Kinship Source==
==Kinship Source==
===--kinPedigree===
* If --kinPedigree is used, pedigree structure coded in [[RAREMETALWORKER#PED_and_DAT_Files | '''PED''']] file is used to generate a kinship matrix for later fitting linear mixed model before associations.
===--kinGeno===
* If --kinPedigree is used, then a genomic relationship matrix is estimated from genotype.
* If --vcX option is used, then a separate genomic relationship matrix for chromosome X is also estimated.
* For details about how to estimate GRM, please refer to [[RAREMETALWORKER_method#MODELING_RELATEDNESS | ''methods''']].
===--kinFile===
* --kinFile takes a string of the file name of previously saved GRM with format described in [[RAREMETALWORKER#Genomic_Relationship_Matrix_.28GRM.29 | '''format''']].
* This option reads GRM from the file and then extract the correct GRM based on samples to be analyzed according to your specifications, such as traits to be analyzed, missing covariates and genotypes (please refer to [[RAREMETALWORKER_SPECIAL_TOPICS#Missing_Data | '''missing data''']] for more details).
* --kinFile can not be used together with --kinGeno.
===--kinxFile===
===--kinSave===
*For formats of the saved genomic relationship matrix, please refer to [[RAREMETALWORKER#Genomic_Relationship_Matrix_.28GRM.29 | '''format''']].
==Kinship Options==
==Kinship Options==
===--kinMaf===
===--kinMiss===
==Chromosome X==
==Chromosome X==
===--xLabel===
===--xStart===
[2699520]
===--xEnd===
[154931044],
==PhoneHome==
==PhoneHome==
===--noPhoneHome===
===--phoneHomeThinning===
