Home | BioWDL: BamMetrics

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This workflow can be used to collect a variety of metrics from a BAM file. Metrics are collected using picard and samtools.

This workflow is part of BioWDL developed by the SASC team.

Usage

This workflow can be run using Cromwell:

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

Inputs

Inputs are provided through a JSON file. The minimally required inputs are described below and a template containing all possible inputs can be generated using Womtool as described in the WOMtool documentation. See this page for some additional general notes and information about pipeline inputs.

{
  "BamMetrics.reference": {
    "fasta": "The path to the reference fasta file",
    "fai": "The path to the index for the reference fasta",
    "dict": "The path to the dict file for the reference fasta"
  },
  "BamMetrics.outputDir": "The path to the output directory",
  "BamMetrics.bam": {
    "file": "A path to an input BAM file",
    "index": "The path to the index for the ipnut BAM file"
  }
}

In the case of RNAseq samples tho following inputs are also required. By providing these inputs additional RNAseq metrics will be collected.

{
  "BamMetrics.refRefflat": "A path to a Refflat annotation file for the reference",
  "BamMetrics.strandedness": "The strandedness of an RNAseq sample. This should be on of 'None', 'FR' (forward-reverse) or 'RF' (reverse-forward), defaults to 'None'"
}

For targeted sequencing samples the following inputs are also required. By providing these inputs additional targeted PCR metrics will be collected.

{
  "BamMetrics.targetIntervals": "A list of paths to the bed files containing the target regions",
  "BamMetrics.ampliconIntervals": "The path to the bed file containing the amplicon regions"
}

Example

{
  "BamMetrics.reference": {
    "fasta": "/home/user/genomes/human/GRCh38.fasta",
    "fai": "/home/user/genomes/human/GRCh38.fasta.fai",
    "dict": "/home/user/genomes/human/GRCh38.dict"
  },
  "BamMetrics.outputDir": "/home/user/analysis/metrics",
  "BamMetrics.bam": {
    "file": "/home/user/mapping/results/s1.bam",
    "index": "/home/user/mapping/results/s1.bai"
  },
  "BamMetrics.targetIntervals": [
    "/home/user/analysis/target1.bed",
    "/home/user/analysis/target2.bed"
  ],
  "BamMetrics.ampliconIntervals": "/home/user/analysis/amplicon.bed"
}

Dependency requirements and tool versions

Included in the repository is an environment.yml file. This file includes all the tool version on which the workflow was tested. You can use conda and this file to create an environment with all the correct tools.

Output

A directory containing the various metrics collected.

Contact

For any questions about running this workflow and feature requests, please use the github issue tracker or contact the SASC team directly at: sasc@lumc.nl.