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=== Unrelated individuals ===
=== Unrelated individuals ===
* Command are the same as in above example, except each individual has to have a distinct family ID in ped file.
* Commands are the same as in above example, except each individual has to have a distinct family ID in PED file, and their father and mother ids should be "0".
* When you have genotypes from ped and marker information from dat file, and assuming no relatedness in the sample:
* When you have genotypes from ped and marker information from dat file, and assuming no relatedness in the sample:
./Rare-Metal-Worker --ped yours.ped --dat yours.dat --vcf yours.vcf.gz
./Rare-Metal-Worker --ped yours.ped --dat yours.dat --vcf yours.vcf.gz
* When you have genotypes from vcf and covariates and trait information saved in ped and dat file, assuming there is cryptic relatedness in the sample, you should use the following:
./Rare-Metal-Worker --ped yours.ped --dat yours.dat --vcf yours.vcf.gz --kinGeno (# this will handle the individuals as related, and generate kinship matrix from genotype.)
== Q & A ==
== Q & A ==
