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Introduction

nf-core/strelkasomatic is a bioinformatics pipeline that calls somatic mutations from BAM files using Illumina's Manta and Strelka2.

There are 2 steps involved

1. Manta
   • Manta to call candidate small Indels, which can then be used to call somatic SNVs and Indels in the Strelka step (along with a "results" directory under "manta_out/${sample_id}", details in docs/output.md)
2. Strelka
   • Strelka to call the final SNVs and Indels VCF files, output files are published in a "results" directory under "strelka_out/${sample_id}", details in docs/output.md

Dependencies

• Nextflow >= 24.04.2 required

[!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.

• python 2.6+

Installation

git clone git@github.com:Phuong-Le/StrelkaSomatic.git

Usage

[NOT PUBLIC YET] Make sure to test your setup with -profile test before running the workflow on actual data.

The input sample sheet should be either in a tab delimited format (extension must be .tsv), or comma delimited format (extension must be .csv), like samplesheet.tsv. Your input should contain the following columns (column names must be accurate but no need to be in this order, redundant columns will be ignored)

| Column | Description | | --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | sample_id | sample ID, must be unique | | match_normal_id | ID for your match normal sample | | | bam | bam file for sample_id, must exist | | | bai | tabix index file for bam, must exist | | bam_match | bam file for match_normal_id, must exist | | bai_match | tabix index file for bam_match, must exist |

Please find the detailed instructions to run the pipeline, including the input parameters in docs/usage.md. You can run the pipeline using:

```bash

nextflow run /path/to/SangerSomaticMutation/main.nf \ -profile \ --input /path/to/samplesheet.csv \ --fasta /path/to/fasta/genome.fa \ --fai /path/to/fai/genome.fa.fai \ --outdir /path/to/outdir ```

If using igenomes please add the following to the nextflow run, note that igenomes do not have the tabix index file for $fasta so you will have to specify this, for example

bash --igenomes_ignore false \ --fai /path/to/fai/genome.fa.fai \ --genome your_genome_label

[!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Sanger users

Sanger users can run the pipeline as follows. Please refer to docs/sanger.md to ensure you have the right set up.

```bash module load cellgen/nextflow/24.10.2

outdir=/path/to/outdir workdir=/path/to/working_directory # where a work directory is created script=/path/to/StrelkaSomatic/main.nf mkdir -p $workdir input=/path/to/samplesheet.tsv fasta=/path/to/fasta/genome.fa fai=/path/to/fasta/index/genome.fa.fai

config=/path/to/StrelkaSomatic/conf/sanger_lfs.config

bsub -cwd $workdir -q long -o %J.o -e %J.e -R'span[hosts=1] select[mem>10000] rusage[mem=10000]' -M10000 -env "all" \ "nextflow run ${script} -c ${config} --input ${input} --outdir ${outdir} --fasta ${fasta} --fai ${fai} -resume" ```

or as follows

```bash module load cellgen/nextflow/24.10.2

outdir=/path/to/outdir workdir=/path/to/workingdirectory # where a work directory is created script=/path/to/StrelkaSomatic/main.nf mkdir -p $workdir input=/path/to/samplesheet.tsv customgenomebase=/lustre/scratch124/casm/team78pipelines/canpipe/live/ref/Homosapiens # please let me know if you're using a different genome so I can update the config for you usecustomgenome=true genome=GRCh38fullanalysissetplusdecoyhla

config=/path/to/StrelkaSomatic/conf/sanger_lfs.config

bsub -cwd $workdir -q long -o %J.o -e %J.e -R'span[hosts=1] select[mem>10000] rusage[mem=10000]' -M10000 -env "all" \ "nextflow run $script -c ${config} --input ${input} --outdir ${outdir} --usecustomgenome ${usecustomgenome} --customgenomebase ${customgenomebase} --genome ${genome} -resume" ```

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/strelkasomatic was originally written by Phuong Le.

We thank the following people for their extensive assistance in the development of this pipeline:

Stephen Fitzgerald

Citations

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