🐍 hydra-genetics/parabricks

Snakemake module containing an array of steps provided by the parabricks tookit

💬 Introduction

The module contains rules to align .fastq-files and call variants in the resulting .bam-files using Clara Parabricks. To use this module a server with access to one or more compatible NVIDIA GPUs is required. Input data should be trimmed .fastq-files and we recommend to generate these with hydra-genetics/prealignment for a smooth transition. In order to make use of read group information, add machine, flowcell and library specifics to units.tsv.

❗ Dependencies

In order to use this module, the following dependencies are required:

🎒 Preparations

Sample and unit data

Input data should be added to samples.tsv and units.tsv. The following information need to be added to these files:

Column Id	Description
samples.tsv
sample	unique sample/patient id, one per row
tumor_content	ratio of tumor cells to total cells
units.tsv
sample	same sample/patient id as in samples.tsv
type	data type identifier (one letter), can be one of Tumor, Normal, RNA
platform	type of sequencing platform, e.g. NovaSeq
machine	specific machine id, e.g. NovaSeq instruments have @Axxxxx
flowcell	identifer of flowcell used
lane	flowcell lane number
barcode	sequence library barcode/index, connect forward and reverse indices by +, e.g. ATGC+ATGC
fastq1/2	absolute path to forward and reverse reads
adapter	adapter sequences to be trimmed, separated by comma

Reference data

Reference files should be specified in config.yaml in the section reference. A .fasta-file is needed as well as a .vcf file containing known indels used during the alignment process. For the RNA alignment part, genome_dir should specify a directory containing reference files generated by STAR.

🚀 Usage

To use this module in your workflow, follow the description in the snakemake docs. Add the module to your Snakefile like so:

module parabricks:
    snakefile:
        github(
            "hydra-genetics/parabricks",
            path="workflow/Snakefile",
            tag="1.0.0",
        )
    config:
        config


use rule * from parabricks as parabricks_*

Compatibility

Latest:

• prealignment:v1.1.0

See COMPATIBLITY.md file for a complete list of module compatibility.

Output files

The following output files should be targeted via another rule:

File	Description
parabricks/pbrun_deepvariant/{sample}.vcf	variant call file generated by deepvariant
parabricks/pbrun_fq2bam/{sample}_{type}.bam	alignment file generated by BWA-mem
parabricks/pbrun_mutectcaller_t/{sample}_T.vcf	variant call file generated by Mutect2 using tumor-only mode
parabricks/pbrun_mutectcaller_tn/{sample}.vcf	variant call file generated by Mutect2 using tumor/normal mode
parabricks/pbrun_rna_fq2bam/{sample}_R.bam	alignment file generated by STAR

🧑‍⚖️ Rule Graph