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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

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