Upgrades and default settings to SomaticStandard

hammerlab / guacamole

Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly

Apache License 2.0

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Upgrades and default settings to SomaticStandard #612

Closed arahuja closed 7 years ago

arahuja commented 7 years ago

This PR updates SomaticStandard to:

compute likelihoods for tumor variants by taking into account empirical (possibly low) VAFs
add separate thresholds for tumor and normal LOD
sets reasonable default on filters and threshold to ensure a good variant set
updates the tests to reflect these

coveralls commented 7 years ago

Coverage decreased (-0.2%) to 78.822% when pulling 495078781819be43c4adf92b617f914218f10393 on arahuja:somatic-standard-upgrades-continue into 9503138ef8f77c0a2b4db82257fa6c12db6a46c5 on hammerlab:master.

coveralls commented 7 years ago

Coverage decreased (-0.4%) to 78.674% when pulling d7cd482d7a13f7cfa5bdce78be5c4a5332c703fd on arahuja:somatic-standard-upgrades-continue into 9503138ef8f77c0a2b4db82257fa6c12db6a46c5 on hammerlab:master.

ryan-williams commented 7 years ago

Superseded by #613

arahuja commented 7 years ago

Is https://github.com/arahuja/guacamole/pull/2 not needed then? Was this merged in in #613?

ryan-williams commented 7 years ago

That's right, sry I didn't garbage-collect!