bolt implements the UMCCR WGS post-processing logic and supporting functionality, and is used extensively throughout the
UMCCR workflow sash.
The post-processing logic is organised into individual processing steps, which are collectively grouped according to the
type of data processed. Each processing step is accessible through specific bolt commands (see Available
commands for the complete listing) and can be run in isolation. Processing steps are integrated
into a production workflow in the sash pipeline.
| Command | Purpose |
|---|---|
bolt smlv_germline prepare |
Select variants given a genome regions file |
bolt smlv_germline report |
Generate summary statistics and CPSR report |
| Command | Purpose |
|---|---|
bolt smlv_somatic rescue |
Supplement DRAGEN calls with SAGE calls and info |
bolt smlv_somatic annotate |
Annotate variants with PCGR, PON, and defined genomic regions |
bolt smlv_somatic filter |
Set and apply filters for variants |
bolt smlv_somatic report |
Generate summary statistics and PCGR report |
| Command | Purpose |
|---|---|
bolt sv_somatic annotate |
Annotate SVs (and CNVs) with SnpEff |
bolt sv_somatic prioritise |
Prioritise variants with rank ordering using prioritize_sv |
| Command | Purpose |
|---|---|
bolt other cancer_report |
Generate the UMCCR Cancer Report |
bolt other multiqc_report |
Generate the MultiQC report |
bolt other purple_baf_plot |
Create a modified PURPLE plot with β-allele frequencies |
For convenience, several Docker images are provided to run bolt aimed at balancing image size with the complexity of
the software environment and dependencies. Consequently, dependencies are split across six images:
| Name | Docker image URI | Commands |
|---|---|---|
| pcgr | ghcr.io/scwatts/bolt:0.2.13-pcgr | • bolt smlv_germline report• bolt smlv_somatic annotate• bolt smlv_somatic report |
| gpgr | ghcr.io/scwatts/bolt:0.2.13-gpgr | • bolt other cancer_report |
| snpeff | ghcr.io/scwatts/bolt:0.2.13-snpeff | • bolt sv_somatic annotate |
| circos | ghcr.io/scwatts/bolt:0.2.13-circos | • bolt other purple_baf_plot |
| multiqc | ghcr.io/scwatts/bolt:0.2.13-multiqc | • bolt other multiqc_report |
| base | ghcr.io/scwatts/bolt:0.2.13 | • bolt smlv_germline prepare• bolt smlv_somatic rescue• bolt smlv_somatic filter• bolt sv_somatic prioritise |
Given the nature of software dependencies required, it is strongly recommended to run bolt commands via the existing
Docker images:
docker run -ti -v $(pwd):$(pwd) -w $(pwd) ghcr.io/scwatts/bolt:0.2.13 \
bolt smlv_somatic filter \
--tumor_name tumor_sample \
--vcf_fp tumor_sample.vcf.gz \
--output_dir ./