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Copy file name to clipboardExpand all lines: help/USAGE.md
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@@ -84,7 +84,7 @@ You can access it by heading to the _Variant calls_ tab and searching your job i
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Click on the alias of the job you want to analyze and you'll be presented with a table reporting various information of the job.
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If the status is <spanstyle="color:#237804">Completed</span>, then you can access and download the output VCF that will be in the _Output files_ row.
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By clicking the name of the output file (usually `malva.vcf`) you'll download the VCF file, whereas by clicking on the _Show in tabular form_ button you'll be redirected to another page that describes the VCF and that highlights the differences between the reference genome and the strain under analysis.
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By clicking the name of the output file, you'll download the VCF file, whereas by clicking on the _Show in tabular form_ button you'll be redirected to another page that describes the VCF and that highlights the differences between the reference genome and the strain under analysis.
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In this page, by default only the wild-type variants detected in the strain are shown, to see all the variants uncheck the _Show only loci with alt.~allele_ filter.
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If the variant catalog was built on a preloaded reference, then you can also view the (summarized) effect of each variant in the _Effect_ column. The full effects predicted by SnpEff for that variant can be accessed by clicking on the summarized effect.
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Moreover, last column is color coded based on the quality of the call.
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