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Revision as of 12:00, 15 June 2014
, 12:00, 15 June 2014→Examining GotCloud SnpCall Output
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[[File:gcsnpcallOut.png|500px]]
[[File:gcsnpcallOut.png|500px]]
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Let's look at the vcfs directory:
ls ${OUT}/vcfs
Just a <code>chr22</code> directory, so look inside of there:
ls ${OUT}/vcfs/chr22
;Can you identify the final filtered VCF and the associated summary file?
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* Answer & annotated directory listing:
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<li>Filtered VCF (SVM & hard filters): chr22.filtered.vcf.gz</li>
<li>Summary file: chr22.filtered.sites.vcf.summary</li>
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[[File:vcfsout.png|600px]]
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Now, let's look in the split directory for the VCF with just the passing variants:
ls ${OUT}/split/chr22
;Which file do you think is the one you want?
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* Answer:
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<li>chr22.filtered.PASS.vcf.gz</li>
</ul>
[[File:splitOut.png|600px]]
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=== Filtered VCF ===
Let's look at the filtered sites file.
less -S ${OUT}/vcfs/chr22/chr22.filtered.sites.vcf
* Scroll down until you find some variants.
** Use space bar to jump a full page
** Use down arrow to move down one line
* Scroll right: lots of info fields, but no per sample genotype information
;What is the first filtered variant that you find?
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* Answer:
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[[File:SvmFilt.png|550px]]
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Remember, use <code>'q'</code> to exit out of <code>less</code>
q
== GotCloud Genotype Refinement ==
== GotCloud Genotype Refinement ==
${GC}/gotcloud ldrefine --conf ${IN}/gotcloud.conf --numjobs 2 --region 22:36000000-37000000
${GC}/gotcloud ldrefine --conf ${IN}/gotcloud.conf --numjobs 2 --region 22:36000000-37000000
