Sarek: A Nextflow repository from moskalenko

Implementing Sarek Pipeline on the University of Florida High Performance Computing Environment

University of Florida High Performance Computing Implementation of Sarek's Pipeline to detect germline or somatic variants from normal or tumour/normal whole-genome, whole exome, or targeted sequencing.

The original Sarek repository has been modified to run on the UF HPC/HiPerGator and instructions are given below.

Create an University of Florida Research Computing Account

First, sign up for UFRC account here.

Connect to UFRC Environment (HiPerGator) Using Your Gatorlink Username and Password.

ssh username@hpg.rc.ufl.edu

Download Modified Sarek Pipeline From This Repository

git clone --recursive https://github.com/jongtaek-kim/Sarek UFRC-Sarek
cd UFRC-Sarek

Setup your UFRC Environment For Interactive Testing Of Sarek Pipeline and Nextflow Script

$ module load ufrc
$ srundev --time=01:00:00
$ module load nextflow/0.32.0
$ module load singularity/2.5.2

Scheduling Jobs On The HiPerGator Using SLURM

The configuration files have been modified for HiPerGator and a sample SLURM script is provided here.

More Updates Coming

For More Information About Sarek Repository and Pipeline, See Below.

An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing

Introduction

Previously known as the Cancer Analysis Workflow (CAW), Sarek is a workflow designed to run analyses on WGS data from regular samples or tumour / normal pairs, including relapse samples if required.

It's built using Nextflow, a domain specific language for workflow building. Software dependencies are handled using Docker or Singularity - container technologies that provide excellent reproducibility and ease of use. Singularity has been designed specifically for high-performance computing environments. This means that although Sarek has been primarily designed for use with the Swedish UPPMAX HPC systems, it should be able to run on any system that supports these two tools.

Sarek was developed at the National Genomics Infastructure and National Bioinformatics Infastructure Sweden which are both platforms at SciLifeLab. It is listed on the Elixir - Tools and Data Services Registry.

Workflow steps

Sarek is built with several workflow scripts. A wrapper script contained within the repository makes it easy to run the different workflow scripts as a single job. To test your installation, follow the tests documentation.

Raw FastQ files or aligned BAM files (with or without realignment & recalibration) can be used as inputs. You can choose which variant callers to use, plus the pipeline is capable of accommodating additional variant calling software or CNV callers if required.

The worflow steps and tools used are as follows:

Preprocessing - main.nf (based on GATK best practices)
- Map reads to Reference
  - BWA
- Mark Duplicates
  - GATK MarkDuplicates
- Base (Quality Score) Recalibration
  - GATK BaseRecalibrator
  - GATK ApplyBQSR
Germline variant calling - germlineVC.nf
- SNVs and small indels
  - GATK HaplotyeCaller
  - Strelka2
- Structural variants
  - Manta
Somatic variant calling - somaticVC.nf (optional)
- SNVs and small indels
- Structural variants
  - Manta
- Sample heterogeneity, ploidy and CNVs
  - ASCAT
Annotation - annotate.nf (optional)
- Variant annotation
  - SnpEff
  - VEP (Variant Effect Predictor)
Reporting - runMultiQC.nf
- Reporting
  - MultiQC

Documentation

The Sarek pipeline comes with documentation in the docs/ directory:

Contributions & Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on Gitter or contact us: maxime.garcia@scilifelab.se, szilveszter.juhos@scilifelab.se

CHANGELOG

CHANGELOG

Credits

Main authors:

Helpful contributors:

moskalenko/Sarek