Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Updated M2 with latest Funcotator info. #5735

Merged
merged 2 commits into from
Feb 28, 2019
Merged

Updated M2 with latest Funcotator info. #5735

merged 2 commits into from
Feb 28, 2019

Conversation

jonn-smith
Copy link
Collaborator

Now the Mutect2 WDL has all the hooks to run Funcotator (Funcotator.wdl was updated as well).

The Funcotate task in the M2 WDL is identical to that same task in Funcotator.wdl.

Fixes #5253

@jonn-smith jonn-smith added this to the Engine-Q12019 milestone Feb 27, 2019
davidbenjamin
davidbenjamin reviewed Feb 27, 2019
View reviewed changes
Copy link
Contributor

@davidbenjamin davidbenjamin left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Just typos, basically. You can merge without sending back.

docs/funcotator/forum_info/forum_post_tutorial.md Outdated
@@ -112,19 +114,73 @@ Versioned gzip archives of data source files are provided here:

<a name="1.1.2.2"></a>
### 1.1.2.2 - gnomAD
The pre-packaged data sources include gnomAD, a large database of known variants. gnomAD is split into two parts - one based on exome data, one based on whole genome data.
The pre-packaged data sources include a subset gnomAD, a large database of known variants. This subset contains a set of INFO fields, primarily containing allele frequency data. gnomAD is split into two parts - one based on exome data, one based on whole genome data. These two data sources are not equivalent and for complete coverage using gnomAD, we recommend annotating with both.
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

subset of gnomAD

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Specify that the subset of INFO fields is much smaller than the original vcf. It is, right?

Copy link
Collaborator Author

@jonn-smith jonn-smith Feb 28, 2019 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Good catch!

Yes - those fields were reduced greatly.

scripts/mutect2_wdl/mutect2.wdl Outdated
## funco_transcript_selection_mode: How to select transcripts in Funcotator. ALL, CANONICAL, or BEST_EFFECT
## funco_output_format: "MAF" to produce a MAF file, "VCF" to procude a VCF file. Default: "MAF"
## funco_compress: (Only valid if funco_output_format == "VCF" ) If true, will compress the output of Funcotator. If false, produces an uncompressed output file. Default: false
## funco_use_gnomad_AF: If true, wil include gnomAD allele frequency annotations in output by connecting to the internet to query gnomAD (this impacts performance). If false, will not annotate with gnomAD. Default: false
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

will include with an extra 'l' in "will"

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Fixed!

@codecov-io
Copy link

codecov-io commented Feb 27, 2019 •
edited
Loading

Codecov Report

Merging #5735 into master will decrease coverage by 6.808%.
The diff coverage is n/a.

@@               Coverage Diff               @@
##              master     #5735       +/-   ##
===============================================
- Coverage     87.061%   80.253%   -6.808%     
+ Complexity     31880     30235     -1645     
===============================================
  Files           1940      1940               
  Lines         146804    146818       +14     
  Branches       16234     16237        +3     
===============================================
- Hits          127809    117826     -9983     
- Misses         13073     23281    +10208     
+ Partials        5922      5711      -211
Impacted Files Coverage Δ Complexity Δ
...kers/filters/VariantFiltrationIntegrationTest.java 0.826% <0%> (-99.174%) 1% <0%> (-25%)
...dorientation/CollectF1R2CountsIntegrationTest.java 0.917% <0%> (-99.083%) 1% <0%> (-12%)
.../walkers/bqsr/BaseRecalibratorIntegrationTest.java 1.031% <0%> (-98.969%) 1% <0%> (-7%)
...ers/vqsr/FilterVariantTranchesIntegrationTest.java 1.053% <0%> (-98.947%) 1% <0%> (-5%)
...s/variantutils/VariantsToTableIntegrationTest.java 1.205% <0%> (-98.795%) 1% <0%> (-20%)
...ientation/ReadOrientationModelIntegrationTest.java 1.667% <0%> (-98.333%) 1% <0%> (-5%)
...on/FindBreakpointEvidenceSparkIntegrationTest.java 1.754% <0%> (-98.246%) 1% <0%> (-6%)
...bender/tools/spark/PileupSparkIntegrationTest.java 2.041% <0%> (-97.959%) 2% <0%> (-13%)
...tute/hellbender/tools/FlagStatIntegrationTest.java 2.083% <0%> (-97.917%) 1% <0%> (-5%)
...rs/variantutils/SelectVariantsIntegrationTest.java 0.25% <0%> (-97.75%) 1% <0%> (-70%)
... and 157 more

@jonn-smith jonn-smith removed the request for review from LeeTL1220 February 28, 2019 18:57
@jonn-smith jonn-smith merged commit 332a560 into master Feb 28, 2019
@jonn-smith jonn-smith deleted the jts_funcotator_wdl_5253 branch February 28, 2019 18:59
@davidbenjamin davidbenjamin mentioned this pull request Mar 1, 2019
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@davidbenjamin davidbenjamin davidbenjamin approved these changes

Assignees

@davidbenjamin davidbenjamin

Labels
Funcotator
Projects
None yet
Milestone
Engine-Q12019
Development

Successfully merging this pull request may close these issues.
3 participants
@jonn-smith @codecov-io @davidbenjamin