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Feature/grch38 3 #952

Merged
merged 10 commits into from
Sep 3, 2019
Merged

Feature/grch38 3 #952

merged 10 commits into from
Sep 3, 2019

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henrikstranneheim
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This PR fixes:

  • Fixes grch38 support processing wise from fastq to ranked variants
  • Still some reference and files need to be built to make a complete workflow Support for hg38 from fastq to ranked variants #95
  • Spidex need to be replaced with another splice tool
  • Rank models are updated but WIP since the necessary input needs to be built or formally rejected.

How to test:

  • Automatic and continuous test pass

Expected outcome:

  • Installation, unit and integration tests pass

Review:

  • Code review
  • New code is executed and covered by tests
  • Tests pass

@henrikstranneheim
feat(grch38): Added grch38 download of genomcs_superDups and modified
db45696 
post processing accordingly
@henrikstranneheim
feat(grch38): Fix hgncd_id format change from VEP CSQ
85abbc4
@henrikstranneheim
feat(grch38): Modifed grch37 default for snpsift
a526f74
@henrikstranneheim
feat(grch38): Added modifications to download script to enable grch38
e30eac6 
post processing of dbnsfp

- Minor refactoring of unzip and gzip
@henrikstranneheim
feat(grch38_dbnsfp): Added new postprocessing to dbnsfp
334b653 
- Added dbnsfp as VEP plugin
- Added new parameter for dbnsfp path for VEP plugin
@henrikstranneheim
feat(grch38): Updated changelog with downstream breaking changes when
81e3585 
using grch38
@henrikstranneheim
feat(grch38): Modified dbnsfp parameter in snpeff
3fd9ffb
@henrikstranneheim
feat(grch38): Made snpsift dbsnfp annotations not mandatory
4c8b663
@henrikstranneheim
feat(grch38_3): Added grch38 config for rd dna
988889a
jemten
jemten approved these changes Sep 3, 2019
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The grch38 goal is getting closer to completion :)

@henrikstranneheim
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Fixed travis in develop

@henrikstranneheim henrikstranneheim merged commit 9382f4c into develop Sep 3, 2019
@henrikstranneheim henrikstranneheim deleted the feature/grch38_3 branch September 3, 2019 10:22
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@jemten jemten jemten approved these changes

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@henrikstranneheim @jemten