Changes

* Another option is to use VCF as input. Please refer to the following link for VCF file specification: [http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 1000 genome wiki VCF specs]  

* Another option is to use VCF as input. Please refer to the following link for VCF file specification: [http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 1000 genome wiki VCF specs]  

* VCF file should be compressed by bgzip and indexed by tabix, using the following command:

* VCF file should be compressed by bgzip and indexed by tabix, using the following command:

   bgzip input.vcf    ## this command will produce input.vcf.gz

   bgzip input.vcf    ## this command will generate input.vcf.gz

   tabix -p vcf -f input.vcf.gz  ## this command will produce input.vcf.gz.tbi

   tabix -p vcf -f input.vcf.gz  ## this command will generate input.vcf.gz.tbi

* Even with the presence of VCF file, PED/DAT files are still needed for covariates and phenotypes.

* Even with the presence of VCF file, PED/DAT files are still needed for covariates and phenotypes.