Exercise 2: Run nf-core/sarek using a second family trio data (HapMap; Genome in a Bottle)
The pipeline requires preparing at least 2 files:
...
Now that we have experience running a couple of case studies, let’s prepare to run the variant calling pipeline for a second family trio. Use the guide for other cases to prepare and submitted the nf-core/sarek pipeline.
Data location:
| Code Block |
|---|
/work/training/sarek/data/trio2 |
Launch script:
| Code Block |
|---|
/work/training/sarek/scripts/launch_sarek_trio2.pbs |
If you have any questions, please ask to one of our friendly trainers.