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The variant calling pipeline generates an initial list of polymorphic sites and genotypes stored in a VCF file and then uses haplotype information to refine these genotypes in an updated VCF file.
The variant calling pipeline generates an initial list of polymorphic sites and genotypes stored in a VCF file and then uses haplotype information to refine these genotypes in an updated VCF file.
== Example Dataset ==
== STEP 1 : Install GotCloud ==
In order to run this tutorial, you need to make sure you have GotCloud is installed on your system.
Installation instructions [[GotCloud#Setup|here]].
=== Example Dataset ===
Our dataset consists of 60 individuals from GBR sequenced by the 1000 Genomes Project. These individuals have been sequenced to an average depth of about 4x.
Our dataset consists of 60 individuals from GBR sequenced by the 1000 Genomes Project. These individuals have been sequenced to an average depth of about 4x.
The example dataset we'll be using is included in this tar-ball TBD.
The example dataset we'll be using is included in this tar-ball TBD.
== STEP 2 : Run GotCloud Alignment Pipeline ==
== STEP 2 : Run GotCloud Alignment Pipeline ==
