Tutorials

The tutorials walk you through a simple use case for Parabricks, giving a brief introduction of how it works. You will start by downloading some sample data:

A reference file (Homo_sapiens_assembly38.fasta) and its index
A 'known indels' file and its index
Two FASTQ files
Associated index files

The tutorials then walk through the following steps:

Alignment (FASTA + FASTQ ==> BAM)
Variant calling (BAM ==> VCF)

The tutorials are meant to be simple and straightforward and to only cover a single, specific use case. You should be able to copy and paste the commands into a terminal window and get the same results as shown. The How-Tos cover more general problem solving using Parabricks.

Steps in the Tutorial

Getting The Sample Data
FQ2BAM Tutorial
HaplotypeCaller Tutorial
Cloud Usage Guides