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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 category of variant results you want to analyse. SNPeff groups results by ‘impact’ and variety of other categories. To see which categories you can analyse, run the two three lines above this one: the ‘variant_type’ line:
library(data.table) and `genetable
genetable <- fread(paste0("./results/reports/snpeff/haplotypecaller/", maingroup, "/", maingroup, ".haplotypecaller.filtered_snpEff.genes.txt"), skip = 1, stringsAsFactors = F)gsub`
gsub("variants_effect_", "", colnames(genetable))[5:length(colnames(genetable))]
Now just run the rmarkdown::render(.... line to automatically generate the report.
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