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Genotype Refinement Output
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<li><code>beagle</code> directory: Beagle output</li> : Beagle output<li><code>thunder</code> directory: Thunder output</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>
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Let's take a look at that interesting location we found in the [[SeqShop:_Sequence_Mapping_and_Assembly_Practical#Accessing_BAMs_by_Position|alignment tutorial]] : chromosome 22, positions 36907000-36907100
 
Use tabix to extract that from the VCFs:
${GC}/bin/tabix ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz 22:36907000-36907100 |less -S
 
;Are there any variants in this region?
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<li>Answer:</li>
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<li>Yes!</li>
<li>Positions:</li>
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<li><code>36907001</code>; Ref: T, Alt: C - that's what we saw before</li>
<li><code>36907098</code>; Ref: T, Alt: C - that's what we saw before</li>
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;What is HG00551's genotype at these positions?
#First check which sample number HG00551 is:
zcat ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz |grep "#CHROM"
* That will help you figure out it's genotype.
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<li>Answer:</li>
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<li>It is the first sample</li>
<li><code>0|1</code>: Heterozygous</li>
<li><code>1|1</code>; Homozygous Alt (C)</li>
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