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README.md

ICGC-TCGA-PanCancer BWA Workflow

Overview

This is the workflow for the TCGA/ICGC PanCancer Analysis of Whole Genomes (PCAWG) project that aligns whole genome sequences with BWA-Mem.

For more information about the project overall see the PanCancer wiki space.

More detailed documentation about the production use of this workflow can be found in the PanCancer-Info project where we maintain our production documentation and SOPs.

Building the Worklfow Docker Image

You can also build a Docker image that has the workflow ready to run in it.

docker build -t pcawg-bwa-mem-workflow

Running the Workflow with Cromwell

java -jar cromwell-19.3.jar run pcawg-bwa-mem-workflow.wdl pcawg-bwa-mem-workflow.json

Sample Data

Some synthetic sample data.

Reference Data

We use a specific reference based on GRCh37.

Authors

Contributors

  • Keiran Raine: PCAP-Core and BWA-Mem workflow design
  • Roshaan Tahir: Original BWA-Align workflow design
  • Adam Struck: WDL implementation