Overview
In this section we’ll be revisiting the variant calling workflows from sessions 2 and 3. Specifically we’ll be doing some further analysis of the nfcore/sarek output.
Downloading the sarek results
If you didn’t attend sessions 2 and 3 (or didn’t successfully complete the sarek workflows), you can download the results of successful runs by running the following command in PuTTY:
cd $HOME/workshops mkdir sarek mkdir sarek/runs mkdir sarek/runs/run2_trio cp /work/training/sarek/runs/run2_trio $
This will copy the three
H:/workshop/sarek/runs/run3_liver
G:\Other computers\Home PC\Desktop\QUT\Liver_exome_variants\sarek