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In the ‘2.Setup’ section, you downloaded 3 nfcore/sarek runs to H:/workshop/sarek/runs. These represent sarek variant calling results from the 3 exercises run in session 2:
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SNPeff creates its own variant analysis reports (html reports) for each sample, which can be seen here:
H:/workshop/sarek/runs/run2_trio/results/reports/snpeff/haplotypecaller
We’ll be creating our of reports, with some additional functional information, using R.
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Click ‘Knit’ to generate the report. It will ask you to name the file and ask where to save the file. Call it ‘test’ and save it in H:/workshop
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You will see it generates the test html report.
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In RStudio, select ‘File’ → “Open File”
Browse to H:/workshop/sarek/runs/run3_liver
Select the ‘modify.R’ file and click ‘Open’.
Open the ‘function_report.Rmd’ file in the same way (it’s in the same location as modify.R)
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This tells the script which sample to run the analysis on. Choose a sample from the list of available samples (which are shown if you run the line above this: dir("./results/reports/snpeff/haplotypecaller/"))
line Line 78: variant_type <- "variants_impact_HIGH"
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