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Add clinical variant annotation to germline #401

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jpfeil opened this issue Aug 5, 2016 · 2 comments
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Add clinical variant annotation to germline #401

jpfeil opened this issue Aug 5, 2016 · 2 comments
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@jpfeil
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jpfeil commented Aug 5, 2016

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@fnothaft
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fnothaft commented Aug 5, 2016

Linking this to #335, #280, BD2KGenomics/cgl-docker-lib#163. @jpfeil can you fill this in with the tools you are going to run in the pipeline?

@fnothaft fnothaft mentioned this issue Aug 6, 2016
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jpfeil commented Aug 16, 2016

I will add Oncotator to the pipeline (https://github.com/broadinstitute/oncotator).

jpfeil added a commit that referenced this issue Aug 16, 2016
@jpfeil
Add oncotator and synapse support (resolves #401)
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@jpfeil jpfeil mentioned this issue Aug 16, 2016
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@jpfeil jpfeil self-assigned this Aug 16, 2016
jpfeil added a commit that referenced this issue Aug 17, 2016
@jpfeil
Add oncotator and synapse support (resolves #401)
4d4bfdc
jpfeil added a commit that referenced this issue Aug 17, 2016
@jpfeil
Add oncotator and synapse support (resolves #401)
889e4e5
jpfeil added a commit that referenced this issue Aug 17, 2016
@jpfeil
Add oncotator and synapse support (resolves #401)
4b2dd4d
jpfeil added a commit that referenced this issue Aug 17, 2016
@jpfeil
Add oncotator and synapse support (resolves #401)
5badb3a
jpfeil added a commit that referenced this issue Aug 17, 2016
@jpfeil
Add oncotator and synapse support (resolves #401)
dfd31c4
jpfeil added a commit that referenced this issue Aug 19, 2016
@jpfeil
Add oncotator and synapse support (resolves #401)
593e2f7
jpfeil added a commit that referenced this issue Aug 21, 2016
@jpfeil
Add oncotator and synapse support (resolves #401)
fd9ef68
jpfeil added a commit that referenced this issue Aug 21, 2016
@jpfeil
Add oncotator and synapse support (resolves #401)
5158c26
jpfeil added a commit that referenced this issue Aug 25, 2016
@jpfeil
Add oncotator and synapse support (resolves #401)
aa2399b
jpfeil added a commit that referenced this issue Sep 3, 2016
@jpfeil
Add oncotator and synapse support (resolves #401)
d04bfb6
jpfeil added a commit that referenced this issue Sep 15, 2016
@jpfeil
Add oncotator and synapse support (resolves #401)
9e53272
jpfeil added a commit that referenced this issue Sep 17, 2016
@jpfeil
Add oncotator and synapse support (resolves #401)
97ec4f5
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Finish production germline pipeline (resolves #401) BD2KGenomics/toil-scripts
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@fnothaft @jvivian @jpfeil