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When Funcotator is run in the mutect2.wdl, it should output MAF, not VCF (by default) #4935

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LeeTL1220 opened this issue Jun 21, 2018 · 1 comment
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When Funcotator is run in the mutect2.wdl, it should output MAF, not VCF (by default) #4935

LeeTL1220 opened this issue Jun 21, 2018 · 1 comment
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Funcotator Mutect PRIORITY_HIGH wdl

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@LeeTL1220
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Feature request

Tool(s) or class(es) involved

Funcotator (and M2)

Description

The mutect2 WDL files run Funcotator with MAF output. This happens when Funcotator is turned on.
@LeeTL1220
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Do some testing on complete M2 runs.

@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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