Changes

* 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

   ./raremetalworker --ped yours.ped --dat yours.dat

* When you have genotypes from vcf and covariates and trait information saved in ped and dat file, assuming there is no relatedness in the sample, you should use the following:

* When you have genotypes from vcf and covariates and trait information saved in ped and dat file, assuming there is no relatedness in the sample, you should use the following:

   ./Rare-Metal-Worker --ped yours.ped --dat yours.dat --vcf yours.vcf.gz

   ./raremetalworker --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:

* 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 individuals as related, and generate kinship matrix from genotype.)

   ./raremetalworker --ped yours.ped --dat yours.dat --vcf yours.vcf.gz --kinGeno (# this will handle individuals as related, and generate kinship matrix from genotype.)

== Q & A ==

== Q & A ==