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==== VCF File ====
==== VCF File ====
* Another option is to use VCF as input. Please refer to the following link for VCF file specification:
* 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]]
* 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
