Changes

== Run GotCloud/GenomeSTRiP pipeline ==

== Run GotCloud/GenomeSTRiP pipeline ==

GotCloud/GenomeSTRiP pipeline consists of three separate steps.

GotCloud/GenomeSTRiP pipeline consists of three separate steps.

* Preprocess step : Create metadata summarizing the GC profiles, depth distribution, insert size distribution for accurate discovery and genotyping of structural variants.

* Preprocess step : Create metadata summarizing the GC profiles, depth distribution, insert size distribution for accurate discovery and genotyping of structural variants.

* Discovery step : Perform variant discovery split by region, across all samples. Also, perform variant filtering based on expert knowledge.

* Discovery step : Perform variant discovery split by region, across all samples. Also, perform variant filtering based on expert knowledge.

* Genotyping step : Iterate discovered variants across the samples and calculate the genotype likelihood of for each possible genotype.

* Genotyping step : Iterate discovered variants across the samples and calculate the genotype likelihood of for each possible genotype.

  In addition, if one wants to genotype structural variants from other structural variant caller, there is a step available.

  In addition, if one wants to genotype structural variants from other structural variant caller, there is a step available.

* Third-party Genotyping and Filtering step : Perform genotyping on the variant sites specified by an input VCF, and also perform variant filtering.

* Third-party Genotyping and Filtering step : Perform genotyping on the variant sites specified by an input VCF, and also perform variant filtering.

 

== Run GotCloud SnpCall ==

== Run GotCloud SnpCall ==

  [[File:SnpcallDiagram.png|500px]]

  [[File:SnpcallDiagram.png|500px]]