114
114
Future sprints (Lightning)
 
2020-10-13
2020-09-29
  • Lightning deployment plan / Uploading data specifications
    5056
    5056
    Lightning
    43
    Idea
    6
    Closed
    5
    0.5
    0.5
    114
    -c-a
    43
  • gVCF/VCF Tyler Specification
    7488
    7488
    Lightning
    43
    Idea
    6
    Closed
    5
    1.0
    1.0
    114
    -c-a
    43
  • Implement Annotation database in Sprite
    5002
    5002
    Lightning
    43
    Idea
    6
    Duplicate
    7
    114
    -c-a
    43
  • align2gvcf test suite
    5983
    5983
    Lightning
    43
    Idea
    6
    Closed
    5
    2.0
    2.0
    114
    -c-a
    43
  • [API] Implement GET /callsets/{callset-name}/vcf API call
    7441
    7441
    Lightning
    43
    Idea
    6
    Closed
    5
    114
    -c-a
    43
  • [API] Implement "GET /assemblies" API Calls
    5470
    5470
    Lightning
    43
    Idea
    6
    Closed
    5
    114
    -c-a
    43
  • Ensure GFF to FASTJ in Lightning git repo
    3538
    3538
    Lightning
    43
    Idea
    6
    Closed
    5
    114
    -c-a
    43
  • FASTQ to FASTJ Implementation
    3536
    3536
    Lightning
    43
    Idea
    6
    Closed
    5
    114
    -c-a
    43
  • CGF path vectors have no-calls on end
    5302
    5302
    Lightning
    43
    Bug
    1
    Closed
    5
    2.0
    2.0
    114
    -c-a
    43
  • [gff2fj] Does not correctly label no-calls at end of cytogenetic band
    5903
    5903
    Lightning
    43
    Bug
    1
    Closed
    5
    114
    -c-a
    43
  • [gff2fj] Add in error checks to check common errors and do sanity checks on resulting FastJ files
    5904
    5904
    Lightning
    43
    Idea
    6
    Closed
    5
    114
    -c-a
    43
  • Implement ProbabilisticPCA on Tiled Genomes
    6653
    6653
    Lightning
    43
    Idea
    6
    Closed
    5
    2.5
    2.5
    114
    -c-a
    43
  • Specify/Document how to use Lightning for family analysis
    5336
    5336
    Lightning
    43
    Idea
    6
    Closed
    5
    114
    -c-a
    43
  • Specify lifting-over assemblies that change the tags
    5526
    5526
    Lightning
    43
    Idea
    6
    Closed
    5
    3.0
    3.0
    114
    -c-a
    43
  • Build support for lifting-over assemblies that change the tags
    7440
    7440
    Lightning
    43
    Idea
    6
    Closed
    5
    114
    -c-a
    43
  • [Tyler] Implementation
    7079
    7079
    Lightning
    43
    Idea
    6
    Closed
    5
    3.0
    3.0
    114
    -c-a
    43
  • [Sprite] Polyphen data addition to annotations
    4070
    4070
    Lightning
    43
    Idea
    6
    Closed
    5
    114
    -c-a
    43
  • Test the effect of phasing imputation workflow
    13376
    13376
    Lightning
    43
    Idea
    6
    Resolved
    3
    114
    -c-a
    43
  • Write phasing imputation workflow
    13216
    13216
    Lightning
    43
    Idea
    6
    Resolved
    3
    114
    -c-a
    43
246
246
Tiling Future
 
no end
no start
  • FastJ aggregation into SGLF takes too much memory
    12951
    12951
    Lightning
    43
    Bug
    1
    New
    1
    246
    -c-a
    43
  • [API] Implement GET /callsets/{callset-name}/gvcf API call
    5334
    5334
    Lightning
    43
    Idea
    6
    New
    1
    246
    -c-a
    43
  • [API] Implement filtering on API calls
    5331
    5331
    Lightning
    43
    Idea
    6
    New
    1
    1.0
    1.0
    246
    -c-a
    43
  • [API] [Documentation] Specify how to find the variants in a gene
    5335
    5335
    Lightning
    43
    Idea
    6
    New
    1
    246
    -c-a
    43
  • [Documentation] [Sprite] [API] Specify API Calls and Database for phenotypes in Sprite
    5332
    5332
    Lightning
    43
    Idea
    6
    New
    1
    2.0
    2.0
    246
    -c-a
    43
  • [Documentation] Specify batch API-like queries
    5330
    5330
    Lightning
    43
    Idea
    6
    New
    1
    2.0
    2.0
    246
    -c-a
    43
  • Create a API interface to the public tile library including a "beacon"
    5001
    5001
    Lightning
    43
    Idea
    6
    New
    1
    5.0
    5.0
    246
    -c-a
    43
  • Specify GA4GH API Implementation with Lightning
    5371
    5371
    Lightning
    43
    Idea
    6
    New
    1
    2.0
    2.0
    246
    -c-a
    43
  • Package lightning specifically for users
    4995
    4995
    Lightning
    43
    Idea
    6
    New
    1
    5.0
    5.0
    246
    -c-a
    43
  • Automatic Deployment Implementation
    4827
    4827
    Lightning
    43
    Idea
    6
    New
    1
    5.0
    5.0
    246
    -c-a
    43
244
244
Tiling 1.0
 
no end
no start
  • pasta rotini-fastj does not handle tagset without ending newline
    12245
    12245
    Lightning
    43
    Bug
    1
    New
    1
    244
    -c-a
    43
245
245
Tiling 1.1
 
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no start
  • Imputation and phasing flag in CGF data
    13639
    13639
    Lightning
    43
    Idea
    6
    New
    1
    245
    -c-a
    43
  • Create tests for 'tile-npy' programs
    12171
    12171
    Lightning
    43
    Idea
    6
    New
    1
    245
    -c-a
    43
  • Covnert hg19 to FastJ and CGF
    11746
    11746
    Lightning
    43
    Idea
    6
    New
    1
    3.0
    3.0
    245
    -c-a
    43
  • Convert Harvard PGP exome data to CGF
    11675
    11675
    Lightning
    43
    Idea
    6
    New
    1
    245
    -c-a
    43
  • Documentation current speed of concordance and other stats
    10104
    10104
    Lightning
    43
    Idea
    6
    New
    1
    2.0
    2.0
    245
    -c-a
    43
  • [API] Implement GET /callsets/{callset-name}/tile-variants
    5329
    5329
    Lightning
    43
    Idea
    6
    New
    1
    2.0
    2.0
    245
    -c-a
    43
  • Implement annotation on Tile Library
    7267
    7267
    Lightning
    43
    Idea
    6
    New
    1
    3.0
    3.0
    245
    -c-a
    43
  • Annotate Tiling 1.0 public library
    7300
    7300
    Lightning
    43
    Idea
    6
    New
    1
    3.0
    3.0
    245
    -c-a
    43
  • Extend CGF to include genotyping
    11673
    11673
    Lightning
    43
    Idea
    6
    New
    1
    1.0
    1.0
    245
    -c-a
    43
  • Convert openSNP genotyping data to CGF
    11674
    11674
    Lightning
    43
    Idea
    6
    New
    1
    4.0
    4.0
    245
    -c-a
    43
Product Backlog
sprint
 
no end
no start
  • 0
    -c-a
    • May 28, 2019 17:34:27.5924239883422852 +0000