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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

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