Changes

==== VCF File ====

==== VCF File ====

=====GENOTYPES=====

=====GENOTYPES=====

* 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 produce input.vcf.gz