WDL descriptors for BRASS and related tooling.
- Please use the git/hub-flow methodology when working in this repository. See this site for details.
- Where applicable please add pre-commit hooks to ensure validation of syntax and linting is applie before commits are pushed.
The official CGP docker repository lives on Quay.io: quay.io/wtsicgp/dockstore-cgpwgs:1.1.3.
WDL does not officially support pulling docker images from Quay yet, so a lagging version is available at Dockerhub: https://hub.docker.com/r/erictdawson/cgp-docker/
[ ] A matched tumor/normal BAM pair, aligned with BWA.
[ ] A set of reference supporting files (e.g. from: ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/CNV_SV_ref_GRCh37d5_brass6+.tar.gz).
[ ] All bam files must have a corresponding .bai file
[ ] All bam files must have a corresponding .bas file
[ ] All bams, indices, and reference files must be in a location accessible to your cloud system (i.e. Google Cloud Storage for FireCloud).
The following workflow description files will produce a BAI/BAS for a given BAM:
- brass-bam-index.wdl
- brass-bam-stats.wdl
A panel of normals improves artifact removal from the final callset.
The inputs of this process are normal-sample BAM files, which are used to generate discordant pair BAMs ("brm-bams"), merged, grouped and indexed.
The following workflow description files will produce PON filter for BRASS.
- brass-generate-brm-bam.wdl
- brass-merge-brm-bams.wdl
- brass-generate-PON-filter.wdl
The following workflow description files will run the main BRASS pipeline on a single cloud VM:
- brass-main.wdl
BRASS will generate a results folder which will contain files containing breakpoint calls (in BEDPE format) and summary statistics such as insert size (in text format).