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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
149 stars 45 forks source link

2020-03-04 9-10 Scout user meeting #1679

Closed dnil closed 4 years ago

dnil commented 4 years ago

KS Solna, BioClinicum, J8:10, Tantal

New features and bugfixes since last time:

  1. Display hgvs coordinates on pinned and causatives
  2. Clear panel pending changes
  3. Fixed ACMG classification not showing for some causatives
  4. Fixed discrepancy between the manual disease transcripts and those in database in gene-edit page
  5. Fixed First IGV button in str variants page
  6. Cancer case activates on SNV variants (also STRs)
  7. Fix bug which caused IGV.js to use hg19 reference files for hg38 data
  8. Drop downs have correct size
  9. SV variant links now take you to the SV variant page again
  10. Cancer variant view has cleaner table data entries for "N/A" data
  11. Fixed same case repetition in variant local observations
  12. Allows for upload of OMIM-AUTO gene panel from static files without api-key
  13. Allows for updating database tables after downloading definition files first.
  14. Editable tumor purity and Tissue type for cancer cases

New bugs since last time:

  1. Missing delivery report for recent cases (fixed in next release)
  2. bug when adding a gene to existing panel (fixed in next release)

Upcoming features in next release

  1. ClinVar SNVs track in IGV
  2. Add SMA view with SMN Copy Number data

MIP CG roadmap - 8.0 / 8.1 / 8.2 - and when you can expect to see the new features in Scout. In production

  1. Turned off bcftools mpileup
  2. Supply CRAM instead of BAM to Scout (70% storage reduction)
  3. Added SMNCopyNumberCaller to MIP for SMN calling with WGS data
  4. Added vcf2cytosure blacklist file for grch37
  5. Multiqc report in Scout
  6. Adds upd for trios
  7. Adds chromograph for chromosome visualization
  8. Automated gender estimation for WGS for samples with unknown gender
  9. Containerized entire workflow
  10. Faster and more efficient processing (WGS 13-17 h)

BALSAMIC CG roadmap: next release

moonso commented 4 years ago

Should we invite cancer people or start up a separate meeting for them?

hassanfa commented 4 years ago

It would be great to include cancer scout + BALSAMIC roadmap as well.

moonso commented 4 years ago

Feel free to add to the agenda @hassanfa 😄

sofievonlanthen commented 4 years ago
  1. Ability to see case numbers from other customers if same variant (without access)?
northwestwitch commented 4 years ago
  1. Activity show variants in a better format (HGVS)
  2. Cosmic track in IGV
  3. Hotspots in IGV
  4. Since there is no pedigree in tumors, rearrange the case panels
  5. Check that tumor samples come from the same individual.
  6. Local observations visualization displayed as frequencies.
  7. Local observations for cancer as well (observations in cancer cases).
  8. Inheritance on top of each other
  9. Gene annotations and gene models together on variant page (on top of each other)