odcf/expansionhunter

Introduction

odcf/expansionhunter is a bioinformatics pipeline to analyse Short Tandem Repeats (STRs) using a combination of Expansion Hunter, samtools, and STRANGER. It is designed to be flexible, supporting various analysis types including single-sample, trio, and somatic cases, and includes an automated sex determination step.

It is designed to be flexible, supporting various analysis types including single-sample, trio, and somatic cases, and includes an automated sex determination step.

Pipeline Description

The pipeline's core logic adapts to your input, following these key steps:

1. Sex Determination: If the sex of a sample is not provided, the pipeline will automatically run the ngs-bits/samplegender tool. This script analyzes the ratio of reads on chromosomes 19, X, and Y to predict the sample's sex.

2. Expansion Hunter: The pipeline runs the Expansion Hunter tool to analyze each sample's BAM file and identify STR expansions.

3. Sample Merging (Conditional): Uses SVDB merge tool.

• Trio Analysis: If you provide three samples (child, father, mother), the pipeline will merge the Expansion Hunter VCF files into a single output.

• Somatic Analysis: For tumor/control sample pairs, the pipeline merges the respective VCF files.

• Single Sample: For a single sample, this merging step is skipped.

1. STRANGER Analysis: The final step runs STRANGER on the merged or single-sample VCF files.

2. MultiQC: Produces final QC reports as well as the versionings of the tools used in this pipeline.

Usage

[!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

1. Download the pipeline and test it on a minimal dataset with a single command:

bash git clone https://github.com/kubranarci/ExpansionHunter.git

1. Set up samplesheet.csv

A samplesheet has to have following columns

sample: The sample name, will be used to create final reports and rename vcf files.

bam: BAM file path to the sample

bai: Index of bam file.

sex: Gender of the sample. Can be female, male, or unknown.

case_id: Case if will be used for trio or somatic analysis to merge and name case samples.

phenotype: Describes the phenotype of the analysis.

• Trio: father, mather or child

• Somatic: tumor or control

• Single: single

samplesheet.csv:

csv sample,bam,bai,sex,case_id,phenotype triofather,triofather.bam,triofather.bam.bai,male,father,triocase triomother,triomother.bam,triomother.bam.bai,female,mother,triocase triochild,triochild.bam,triochild.bam.bai,male,child,triocase somaticcontrol,somaticcontrol.bam,somaticcontrol.bam.bai,unknown,control,somaticcase somatictumor,somatictumor.bam,somatictumor.bam.bai,unknown,tumor,somaticcasecase test,test.bam,test.bam.bai,unknown,single,singlecase

Check out /assets/samplesheet.csv for an example sample sheet file.

1. Prepare reference data

This pipelines needs a fasta reference with fai index and variant catalog file to run Expansion Hunter and Stranger.

• fasta: Path to the FASTA reference
• fai: Path to FAI of FASTA file
• variant_catalog: Path to the variant catalog, GRCh37 and GRCh38 versions from STRANGER can be find in assets/. For more, check https://github.com/Clinical-Genomics/stranger/tree/master/stranger/resources

1. Now, you can run the pipeline using:

bash nextflow run odcf/expansionhunter \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --fasta reference.fa \ --fai reference.fai \ --variant_catalog variant_catalog.json \ --outdir <OUTDIR>

Credits

odcf/expansionhunter was originally written by @kubranarci.

This pipeline was inspired from repeat analysis subworkflow of nf-core/rarediseases pipeline.

Contributions and Support

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

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.