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README_WGS.md

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HMF DNA WGS Example Pipeline

These scripts demonstrate how to run each HMF component in turn to produce DNA variant calling and analysis.

They match the current tool version, configuration and resource files as used in the current HMF GCP pipeline (see Platinum).

Set-up

  1. Download the latest release JAR for each tool as listed here.
  • also ensure that samtools (1.10 or higher) and bwa (0.7.17 or higher) are on the path

  1. Download the resources files for either GRCh37 or GRCh38 from HMFTools-Resources > DNA-Resources. The latest resource files version is v5.31. The reference genome files are available separately HMFTools-Resources > Ref-Genome.

  2. Call the pipeline with the following arguments:

  • a sample tumorId and referenceId (eg 'COLO829T' and 'COLO829R' below)
  • the sample data directory with an existing directory named as per the sample's tumorId
  • tumor and reference BAM and BAM index files in the sample's directory, named as tumorId.bam and referenceId.bam
  • all required tools in a tools directory
  • all required resource files in a resource files directory
  • the reference genome version - either 'V37' or 'V38'
  • whole-genome mode 'WGS' (instead of 'PANEL')
  • number of threads used for each component
  • maximum memory allocated to each component (default=12GB)
./scripts/run_pipeline ./scripts /sample_data/ /ref_data_dir/ /tools_dir/ "COLO829T,COLO829R" V37 WGS 10 16

Test data

A trimmed-down set of GRCh37 BAM files are available for COLO829 here. They cover a few driver variants, a fusion and the HLA regions. The pipeline takes about 10 mins to run on these.

Output

Each component will write its output to a separate directory. Plots for Purple and Linx are generated to './sample/purple/plots' and './sample/linx_somatic/plots'.

COLO829 chr10