BioWDL: structural-variantcalling

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This pipeline merges the SV predictions from Delly, Manta, and Mateclever using SURVIVOR merge.

This pipeline is part of BioWDL developed by the SASC team at Leiden University Medical Center.

Usage

You can run the pipeline using Cromwell:

java -jar cromwell-<version>.jar run -i inputs.json structural-variantcalling.wdl

Inputs

Inputs are provided through a JSON file. The minimally required inputs are described below, but additional inputs are available. A template containing all possible inputs can be generated using Womtool as described in the WOMtool documentation. For overviews of all available inputs, see this page

{
  "SVcalling.outputDir": "The directory the output should be written to.",
  "SVcalling.referenceFasta": "The reference fasta file",
  "SVcalling.referenceFastaFai": "Fasta index (.fai) file of the reference",
  "SVcalling.referenceFastaDict": "Sequence dictionary (.dict) file of the reference",
  "SVcalling.bamFile": "sorted BAM file",
  "SVcalling.bamIndex": "BAM index(.bai) file",
  "SVcalling.bwaIndex": "Struct containing the BWA reference files",
  "SVcalling.sample": "The name of the sample"
}

Example

The following is an example of what an inputs JSON might look like:

{
  "SVcalling.bamIndex": "tests/data/ref_with_svs.bai",
  "SVcalling.sample": "sample",
  "SVcalling.referenceFastaFai": "tests/data/reference/reference.fasta.fai",
  "SVcalling.referenceFasta": "tests/data/reference/reference.fasta",
  "SVcalling.bamFile": "tests/data/ref_with_svs.bam",
  "SVcalling.referenceFastaDict": "tests/data/reference/reference.dict",
  "SVcalling.bwaIndex": {
    "fastaFile": "tests/data/reference/bwa/reference.fasta",
    "indexFiles": [
        "tests/data/reference/bwa/reference.fasta.sa",
        "tests/data/reference/bwa/reference.fasta.amb",
        "tests/data/reference/bwa/reference.fasta.ann",
        "tests/data/reference/bwa/reference.fasta.bwt",
        "tests/data/reference/bwa/reference.fasta.pac"
    ]
  }
}

Dependency requirements and tool versions

Biowdl pipelines use docker images to ensure reproducibility. This means that biowdl pipelines will run on any system that has docker installed. Alternatively they can be run with singularity.

For more advanced configuration of docker or singularity please check the cromwell documentation on containers.

Images from biocontainers are preferred for biowdl pipelines. The list of default images for this pipeline can be found in the default for the dockerImages input.

Output

This pipeline produces VCF files from Delly, Manta, and Mateclever, as well as the merged VCF file from SURVIVOR.

Contact

For any questions about running this pipeline and feature request (such as adding additional tools and options), please use the github issue tracker or contact the SASC team directly at: sasc@lumc.nl.