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https://github.com/mskcc/sif

Nextflow workflow for handling Structural Variants
https://github.com/mskcc/sif

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Nextflow workflow for handling Structural Variants

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[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)

[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)

[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)

[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)

[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/mskcc/sif)



## Introduction



**mskcc/sif** is a bioinformatics pipeline that calculates the structural variants mutations from a Tumor/Normal Bam pair.



![Sif graph](docs/images/Sif.png)



1. Calculate SV variants ([`Delly`](https://github.com/dellytools/delly/releases/tag/v1.2.6))

2. Filter SV variants ([`Delly`](https://github.com/dellytools/delly/releases/tag/v1.2.6))

3. Concat variants ([`bcftools`](https://github.com/samtools/bcftools/tree/1.9))

4. Convert to maf ([`vcf2maf`](https://github.com/mskcc/vcf2maf/releases/tag/v1.6.17))

5. Generate portal file ([`format_maf`](modules/local/format-maf/resources/usr/bin/format_maf.sh))



## Usage



> [!NOTE]

> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.



First, prepare a samplesheet with your input data that looks as follows:



`samplesheet.csv`:



```csv

pairId,tumorBam,normalBam,assay,normalType,bedFile

pair_sample,/bam/path/foo_tumor.rg.md.abra.printreads.bam,/bam/path/foo_normal.rg.md.abra.printreads.bam,IMPACT505,MATCHED,NONE

```



> [!IMPORTANT]

> Make sure the bams have an index file associated with it either file.bam.bai or file.bai should work



Now, you can run the pipeline using:



```bash

nextflow run main.nf \

   -profile singularity,test_juno \

   --input samplesheet.csv \

   --outdir 

```



> [!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](https://nf-co.re/usage/configuration#custom-configuration-files).



## Credits



mskcc/sif was originally written by Nikhil Kumar [@nikhil](https://github.com/nikhil).



## Contributions and Support



If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).



## Citations



An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.



This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).



> **The nf-core framework for community-curated bioinformatics pipelines.**

>

> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

>

> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).