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GotCloud Genotype Refinement
== GotCloud Genotype Refinement ==
To improve the quality of the genotypes, we run a genotype refinement pipeline.
This pipeline runs [http://faculty.washington.edu/browning/beagle/beagle.html Beagle] & thunder.
 
=== Genotype Refinement Input ===
The GotCloud genotype refinement pipeline takes the VCF file of PASS'ing SNPs from snpcall as input.
 
The bam index and the configuration file we used for GotCloud snpcall will tell GotCloud genotype refinement everything it needs to know, so no new input files need to be prepared.
 
=== Running GotCloud Genotype Refinement ===
Since everything is setup, just run the following command (very similar to snpcall).
${GC}/gotcloud ldrefine --conf ${IN}/gotcloud.conf --numjobs 2 --region 22:36000000-37000000
 
* Beagle will take about 2-3 minutes to complete
* Thunder will automatically run and will take another 3-4 minutes
 
=== Genotype Refinement Output ===
 
; What's new in the output directory?
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<li>Answer</li>
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<ul>
<li><code>beagle</code> directory</li> : Beagle output
<li><code>thunder</code> directory</li> : Thunder output
<li><code>umake.beagle.conf</code> : Configuration values used for GotCloud beagle</li>
<li><code>umake.beagle.Makefile</code> : GNU makefile for commands run as part of GotCloud beagle</li>
<li><code>umake.beagle.Makefile.log</code> : Log of the GotCloud beagle run</li>
<li><code>umake.thunder.*</code> files : Contain the configuration & steps used in GotCloud thunder</li>
</ul>
</div>
</div>
</ul>

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