| Table of Contents | ||
|---|---|---|
|
...
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:
...
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.
...
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
...
You will see it generates the test html report.
...
In RStudio, select ‘File’ → “Open File”
Browse to H:/workshop/sarek/runs/run2run3_trioliver
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)
These are the two files you’ll need to generate the reports.G:\Other computers\Home PC\Desktop\QUT\Liver_exome_variants\sarek