Clinical-Genomics/BALSAMIC

Issues

• [User Story] improve IGH-DUX4 presentation in Scout

  #1485 opened 4 months ago by mathiasbio
  1

• [User Story] Improve CNV calling for target workflow

  #1435 opened 9 months ago by ivadym
  5

• d4 file generation (for chanjo2 primarily)

  #1484 opened 4 months ago by dnil
  1

• [User Story] Remove UMI family-size filtering for normal sample

  #1482 opened 5 months ago by mathiasbio
  0

• [User Story] Add MSI analysis

  #1443 opened 8 months ago by khurrammaqbool
  3

• [User Story] Merge VarDict and TNscope results

  #1480 opened 5 months ago by mathiasbio
  0

• [Maintenance] Add QC criteria for bait set Lymphoma MRD

  #1478 opened 5 months ago by moahaegglund
  0

• [User Story] Update TIDDIT to make use of single-end reads

  #1467 opened 7 months ago by mathiasbio
  1

• [User Story] Create TNscope PON

  #1405 opened a year ago by mathiasbio
  1

• [Maintenance] Standardise bait set and capture kit terminology

  #1476 opened 6 months ago by mathiasbio
  1

• [Bug] Enable IGH DUX4 detection for hg38

  #1421 opened 6 months ago by ivadym
  1

• PoN for GMCKsolid v. 4.2

  #1460 opened 8 months ago by moahaegglund
  2

• [User Story] Fix issue with filtered regions in CNVkit

  #1468 opened 7 months ago by mathiasbio
  9

• [User Story] PON for GMSsolid 15.2

  #1474 opened 6 months ago by mathiasbio
  0

• [Bug] Ensure Balsamic is working for hg38

  #1425 opened 10 months ago by mathiasbio
  1

• [User Story] PON for WES Exomecomprehensive 10.2

  #1473 opened 6 months ago by mathiasbio
  0

• [Bug] Sentieon Dedup with UMI consensus BAM issues

  #1472 opened 6 months ago by mathiasbio
  1

• [Assessment] Do we need additional callers for ITD?

  #1399 opened a year ago by mathiasbio
  0

• [Assessment] A lot of bins filtered in CNV analysis

  #1466 opened 7 months ago by mathiasbio
  4

• [User Story] Add Sentieon path argument to case config

  #1462 opened 7 months ago by mathiasbio
  1

• [Bug] Clear variant missing in TNscope T/N WGS case

  #1458 opened 8 months ago by mathiasbio
  3

• Verification Report [v15.0.1]

  #1451 opened 8 months ago by ivadym
  2

• [Maintenance] Update gene model annotation resources

  #1455 opened 8 months ago by dnil
  0

• [User Story] Add adapter trimming to the UMI workflow

  #1440 opened 9 months ago by mathiasbio
  1

• [User Story] Rebuild GENS PON for better X coverage

  #1449 opened 8 months ago by mathiasbio
  0

• [User Story] Remove low-mappability variants from gnomad vcf used for GENS

  #1447 opened 8 months ago by mathiasbio
  0

• [Bug] DNAscope gnomad rule failing due to memory

  #1431 opened 8 months ago by mathiasbio
  2

• [Bug] Fix tmp-dirs in some leaky rules

  #1446 opened 8 months ago by mathiasbio
  1

• [User Story] Ensure up to date Miro board of balsamic exists

  #1445 opened 8 months ago by mathiasbio
  0

• [User Story] Add more SV databases for frequency filtering

  #1442 opened 9 months ago by mathiasbio
  0

• [Assessment] Ensure no strand-bias issues from using UMI-collapsed reads in TNscope

  #1438 opened 9 months ago by mathiasbio
  0

• [User Story] Rebuild PONs with new samples and bioinfo-methods

  #1439 opened 9 months ago by mathiasbio
  0

• [User Story] Parse tumor purity estimate to be fetched for Scout

  #1436 opened 9 months ago by khurrammaqbool
  0

• [User Story] LoqusDB for FFPE samples

  #1437 opened 9 months ago by khurrammaqbool
  0

• [User Story] HRD detection in Balsamic

  #1417 opened a year ago by mathiasbio
  0

• [User Story] Implementation of a unified pre and unified post annotation SV filters

  #1430 opened 10 months ago by khurrammaqbool
  0

• [User Story] Update to GATK 4

  #1409 opened a year ago by pbiology
  0

• [Maintenance] Update Validation Cases Customer and Delivery Type

  #1426 opened 10 months ago by ivadym
  1

• [User Story] Replace VarDict with TNscope

  #1428 opened 10 months ago by mathiasbio
  0

• [Assessment] Do we need to maintain support for canfam3?

  #1427 opened 10 months ago by mathiasbio
  0

• [User Story] Lower stringency for read depth in exome samples

  #1423 opened a year ago by mathiasbio
  1

• [User Story] Change VarDict option to prevent wrong strandbias filtering

  #1415 opened a year ago by mathiasbio
  1

• [User Story] Create PON for lymphoid 7.3

  #1407 opened a year ago by mathiasbio
  11

• Verification Report [v14.0.1]

  #1410 opened a year ago by khurrammaqbool
  5

• [User Story] COSMIC signatures/profiles

  #1416 opened a year ago by mathiasbio
  1

• [User Story] SweGen and CADD reference data

  #1418 opened a year ago by pbiology
  0

• [Assessment] Reanalysis (new downsampling) in BALSAMIC where a variant is missed by VarDict

  #1396 opened a year ago by moahaegglund
  9

• [Assessment] CNV calling in low purity samples

  #1401 opened a year ago by mathiasbio
  1

• [User Story] Fix MaxDepth by adding exome flag for TGA manta analysis

  #1392 opened a year ago by mathiasbio
  1

• [Bug] MulltiQC intermediate JSON files do not store sample id as key

  #1398 opened a year ago by ChrOertlin
  0