The tutorials walk you through a simple use case of Clara Parabricks, giving you a brief introduction to how it works.
You will start by downloading some sample data consisting of:
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 you through the following steps:
Alignment (FASTA + FASTQ ==> BAM)
Variant calling (BAM ==> VCF)
Computation of BAM and VCF metrics
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 Clara Parabricks.