Lightning - Arvados

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5056 5056 Sarah Guthrie Sarah Guthrie 184 Lightning deployment plan / Uploading data specifications Closed Closed 5 0.5 0.5 0.5 5056 43 184 114 6 0.5
7488 7488 gVCF/VCF Tyler Specification Closed Closed 5 1.0 1.0 1.0 7488 43 114 6 1.0
5002 5002 Implement Annotation database in Sprite Duplicate Duplicate 7 5002 43 114 6
5983 5983 align2gvcf test suite Closed Closed 5 2.0 2.0 2.0 5983 43 114 6 2.0
7441 7441 [API] Implement GET /callsets/{callset-name}/vcf API call Closed Closed 5 7441 43 114 6
5470 5470 [API] Implement "GET /assemblies" API Calls Closed Closed 5 5470 43 114 6
3538 3538 Ensure GFF to FASTJ in Lightning git repo Closed Closed 5 3538 43 114 6
3536 3536 FASTQ to FASTJ Implementation Closed Closed 5 3536 43 114 6
5302 5302 Abram Connelly Abram Connelly 99 CGF path vectors have no-calls on end Closed Closed 5 2.0 2.0 2.0 5302 43 99 114 1 2.0
5903 5903 [gff2fj] Does not correctly label no-calls at end of cytogenetic band Closed Closed 5 5903 43 114 1
5904 5904 [gff2fj] Add in error checks to check common errors and do sanity checks on resulting FastJ files Closed Closed 5 5904 43 114 6
6653 6653 Implement ProbabilisticPCA on Tiled Genomes Closed Closed 5 2.5 2.5 2.5 6653 43 114 6 2.5
5336 5336 Specify/Document how to use Lightning for family analysis Closed Closed 5 5336 43 114 6
5526 5526 Specify lifting-over assemblies that change the tags Closed Closed 5 3.0 3.0 3.0 5526 43 114 6 3.0
7440 7440 Build support for lifting-over assemblies that change the tags Closed Closed 5 7440 43 114 6
7079 7079 [Tyler] Implementation Closed Closed 5 3.0 3.0 3.0 7079 43 114 6 3.0
4070 4070 Sarah Guthrie Sarah Guthrie 184 [Sprite] Polyphen data addition to annotations Closed Closed 5 4070 43 184 114 6
13376 13376 Jiayong Li Jiayong Li 303 Test the effect of phasing imputation workflow Resolved Resolved 3 13376 43 303 114 6
13216 13216 Jiayong Li Jiayong Li 303 Write phasing imputation workflow Resolved Resolved 3 13216 43 303 114 6		13215 13215 Write phasing workflow with eagle v2.4 * Build docker image with eagle v2.4 (https://data.broadinstitute.org/alkesgroup/Eagle/downloads/Eagle_v2.4.tar.gz) * Write workflow scattering across reference panels * Test workflow Jiayong Li 303 0 13216 3 43 -c-a 5 13263 13263 Review Abram Connelly 99 0 13216 3 43 -c-a 5 13300 13300 Write phasing workflow with beagle 4.1 * Build docker image with beagle 4.1 (http://faculty.washington.edu/browning/beagle/beagle.27Jan18.7e1.jar) * Write workflow scattering across reference panels * Test workflow Jiayong Li 303 0 13216 3 43 -c-a 5 13334 13334 Review Reviewing branch 13216-phasing-imputation-workflow on l7g-ml with workflows in project su92l-j7d0g-049ipwfxdg21tun Specifically the following runs: * su92l-xvhdp-zb7seb8e430gfmy beagle.cwl * su92l-xvhdp-5kqltvk43tcb984 imputation-wf.cwl * su92l-xvhdp-3v5lgvkm8odwbtb imputation-wf.cwl Keldin Sergheyev 807 0 13216 3 43 -c-a 5