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* --kinPedigree allows Rare-Metal-Worker to generate kinship matrix from pedigree, when pedigree information is available. This option is on by default.
* --kinPedigree allows Rare-Metal-Worker to generate kinship matrix from pedigree, when pedigree information is available. This option is on by default.
* --kinGeno informs Rare-Metal-Worker to generate kinship matrix from all available variants that pass the criteria, specified in --kinMaf and --kinMiss options. The default will take variants with MAF>0.05 and genotype missing rate <0.05.
* --kinGeno informs Rare-Metal-Worker to generate kinship matrix from all available variants that pass the criteria, specified in --kinMaf and --kinMiss options. The default will take variants with MAF>0.05 and genotype missing rate <0.05.
* --kinFile let Rare-Metal-Worker read in a kinship matrix from a file. However, the kinship matrix has to be generated using Rare-Metal-Worker previously.
* --kinFile let Rare-Metal-Worker read in a kinship matrix from a file. However, the kinship matrix has to be generated using Rare-Metal-Worker previously from the same VCF file or EPD/DAT file.
* --kinSave allows you to save the kinship.
* --kinSave allows you to save the kinship.
