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Enable running of Funcotator in the M2 WDL tests. #4807

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LeeTL1220 opened this issue May 24, 2018 · 1 comment
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Enable running of Funcotator in the M2 WDL tests. #4807

LeeTL1220 opened this issue May 24, 2018 · 1 comment
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Funcotator Mutect tests wdl

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@LeeTL1220
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Change the json to enable running of funcotator and fix any errors that occur.
@LeeTL1220
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LeeTL1220 commented May 24, 2018 •
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Do not make any changes re:oncotator .... IMHO

@LeeTL1220 LeeTL1220 self-assigned this May 24, 2018
LeeTL1220 added a commit that referenced this issue May 24, 2018
@LeeTL1220
Fixing #4807 and #4808
581c2e2
@LeeTL1220 LeeTL1220 removed their assignment May 24, 2018
LeeTL1220 added a commit that referenced this issue May 24, 2018
@LeeTL1220
- Added flag to ease restrictions on b37 reference for chr/non-chr co…
f480c17 
…mparisons. This is useful for dev testing.

- Added parsing of funcotation attribute using the VCF Header.  Mostly used for dev testing.

- VCF Datasources now have to match the alt and ref alleles to be condsidered a hit.
- Fixing #4807 and #4808
LeeTL1220 added a commit that referenced this issue May 24, 2018
@LeeTL1220
Reverting fix for #4807, since it was not trivial (still easy) and ou…
9ce5236 
…t of scope for this PR. Also, fixed place where rebasing botched.
@LeeTL1220 LeeTL1220 mentioned this issue Jun 22, 2018
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LeeTL1220 added a commit that referenced this issue Jul 16, 2018
@LeeTL1220
Making MAF become the output of Funcotator in M2 WDL and multiple tra…
1977c53 
…nscript fix. (#4941)

- MAF is the output of Funcotator in M2 WDL.  Closes #4935 
- Updated mutect2.wdl manually tested locally and manually tested in FireCloud.
- Updated mutect2_nio.wdl manually tested in FireCloud.
- Updated automatic Cromwell WDL tests.  Closes #4807 
- Empty MAFs will be devoid of variants, not a file of 0 bytes.  Closes #4937 
- Fixed issue where multiple transcripts could be selected in edge cases, even when CANONICAL or BEST_EFFECT was selected.  Closes #4952
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