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Revision as of 01:11, 18 June 2014
, 01:11, 18 June 2014→Running GotCloud/GenomeSTRiP Discovery Pipeline
[[File:Genomestrip filter description.png|600px]]
[[File:Genomestrip filter description.png|600px]]
== Running GotCloud/GenomeSTRiP Genotyping Pipeline ==
The discovery pipeline only performs discovery of variant sites with filtering. You will need to iterate BAMs again to perform genotyping.
time perl $GC/bin/genomestrip.pl -run-genotype --metadata $IN/metadata --out $OUT/sv --conf $IN/gotcloud.conf --region 22:36000000-37000000 --numjobs 4
This will take ~3 minutes to finish.
You can check the output by running
zless $OUT/sv/genotype/genotype.vcf.gz
You will see output similar to this
<div class="mw-collapsible mw-collapsed" style="width:600px">
You will see the output with genotype information
<div class="mw-collapsible-content" style="width:800px">
[[File:Genomestrip genotype screenshot.png|800px]]
</div>
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== Running GotCloud/GenomeSTRiP 3rd-party Site Genotyping/Filtering Pipeline ==
You can take a 3rd-party site and genotype with GenomeSTRiP. Here we take a 1000 Genomes phase 1 sites and genotype them.
time perl $GC/bin/genomestrip.pl -run-thirdparty --in-vcf $EXT/1kg.phase1.chr22.36Mb.sites.vcf --metadata $IN/metadata --out $OUT/sv --conf $IN/gotcloud.conf --region 22:36000000-37000000 --numjobs 4
This will take ~2 minutes to finish.
You can also check the output by running
zless $OUT/sv/thirdparty/genotype.vcf.gz
<div class="mw-collapsible mw-collapsed" style="width:600px">
You will see the output with genotype information
<div class="mw-collapsible-content" style="width:800px">
[[File:Genomestrip thirdparty screenshot.png|800px]]
</div>
</div>
== What does a real SV look like? ==
samtools tview does not provide a good way to visualize structural variants due to limited resolution to show large-scale variants. IGV provides a good alternative way to visualize structural variants as shown in the xample below.
<div class="mw-collapsible mw-collapsed" style="width:600px">
Do you understand why this is a likely SV?
<div class="mw-collapsible-content" style="width:800px">
[[File:Igvsvexample.png|800px]]
</div>
</div>
== Run GotCloud SnpCall ==
== Run GotCloud SnpCall ==
