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==== VCF File ====
==== VCF File ====
=====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:
* When genotypes are saved in the PED file, the VCF file is not needed. An example command line might look like this:
* When genotypes are saved in the PED file, the VCF file is not needed. An example command line might look like this:
--ped input.ped --dat input.dat
--ped input.ped --dat input.dat
=====DOSAGE=====
* If you want to analyze dosage data from VCF file, the following option has to be specified: --dosage. A key word "DS" in FORMAT field in VCF file has to included accordingly. An example is in the following:
* If you want to analyze dosage data from VCF file, the following option has to be specified: --dosage. A key word "DS" in FORMAT field in VCF file has to included accordingly. An example is in the following:
