0.8 (7 Aug 2018)
- SV filtering: require all of FILTER fields to be PASS or rejected by sv-prioritizer
- SV filtering: always keep SR or PR above 10x regardless of BPI_AF (but above 5x only if BPI_AF>10%)
- SV filtering: check BPI_AF in both breakends
- Add option --no-s3 to skip IGV upload; use it in tests
- Restart failed jobs tree times (helps with PCGR random issues)
- Exlcuding/including samples: perform before check for correct YAML
- Exlcuding/including samples: support {batch}__{sample} identifiers
- Sopport the new and old germline VCF bcbio naming (-.vcf.gz and -germline-.vcf.gz)
0.7 (26 Jun 2018)
- Dockerized version with --docker
- Custom reference data with --pon, --ref-fasta, --truth-regions, or --bcbio-genomes
0.6 (15 May 2018)
- Use snakemake groups to optimize execution on cluster
- Use submission wrapper to automate cluster resources
- Filter structural variants: BPI_AF>=10% and read support>=5
- Keep sv-prioritize hard-filtered variants
- 0.6.1
- Add circos plots into the Rmd report. Generated by https://github.com/umccr/rock
0.5 (7 May 2018)
- PCGR is deployed directly on Spartan, so no AWS dependency.
- Add PCGR wrapper:
pcgr variants.vcf.gz cnv.tsv -o results [-g hg38]
- Correctly providing memory resources on HPC to avoid oom-kill
- On Spartan, support
--cluster-auto
to automatically substitute proper cluster parameters
0.4 (17 Apr 2018)
- Propagate snakemake's cluster options to the wrapper
- Propagate snakemake's
--rerun-incomplete
and to the wrapper - PCGR: stop using the UID, skip uploading if already uploaded
- Fix
HTTP_PROXY
setting for running on Spartan worker nodes - New panel of normals: add the large A5 cohort, normalize normals, check only POS for indels
- Correctly set threads to mibibams samtools runs
0.3 (17 Jan 2018)
- Refactor output folder structure (see docs)
pcgr_download
taget to automatically pull results- Automatically attempt downloading PCGR results after minibams
- Minibams always run in the ned
- Use
--unlock
to automate the snakemake unlock pattern to continue unterrupted runs - Move
vcf_stuff
to a separate repo - Remove GL* chromosomes from the cnvkit diagram
- PCGR tomls: changed mutsignatures_normalization to genome
- Rmd: add SV-prioritize table