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Changed CNV PoN to filter on equality to interval median percentile. #4503

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merged 1 commit into from Apr 4, 2018

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commented Mar 6, 2018

This will require less tuning of minimum-interval-median-percentile to filter out completely uncovered intervals, which will avoid e.g. https://gatkforums.broadinstitute.org/gatk/discussion/11461/gatk-4-0-1-2-no-non-zero-singular-values-were-found-in-creating-a-panel-of-normals-for-somatic-cnv

For example, currently if 10% of my intervals are completely uncovered and I set the relevant parameter to 5%, the 5th percentile is then equal to zero. However, because no intervals are strictly less than zero, none are filtered. Changing this to filter on equality then gets rid of all 10% of the intervals as one would want to do in practice.

@samuelklee samuelklee force-pushed the sl_median_pct branch from dee1b64 to 9a84a34 Mar 7, 2018
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commented Mar 7, 2018

Codecov Report

Merging #4503 into master will decrease coverage by 0.008%.
The diff coverage is 0%.

@@               Coverage Diff               @@
##              master     #4503       +/-   ##
===============================================
- Coverage     79.119%   79.111%   -0.008%     
+ Complexity     16677     16675        -2     
===============================================
  Files           1051      1051               
  Lines          60285     60285               
  Branches        9875      9875               
===============================================
- Hits           47697     47692        -5     
- Misses          8760      8765        +5     
  Partials        3828      3828
Impacted Files Coverage Δ Complexity Δ
...ools/copynumber/CreateReadCountPanelOfNormals.java 90% <ø> (ø) 9 <0> (ø) ⬇️
.../tools/copynumber/denoising/SVDDenoisingUtils.java 79.399% <0%> (ø) 47 <0> (ø) ⬇️
...utils/smithwaterman/SmithWatermanIntelAligner.java 50% <0%> (-30%) 1% <0%> (-2%)
...e/hellbender/engine/spark/SparkContextFactory.java 71.233% <0%> (-2.74%) 11% <0%> (ø)
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commented Mar 7, 2018

An even easier one, @mbabadi!

@samuelklee samuelklee requested a review from mbabadi Mar 7, 2018
@samuelklee samuelklee force-pushed the sl_median_pct branch from 9a84a34 to 73c3f19 Mar 13, 2018
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commented Mar 22, 2018

@mbabadi Can you take a quick look?

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commented Apr 2, 2018

@mbabadi Can we get this in the next release? Should be quick.

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mbabadi approved these changes Apr 3, 2018
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Looks good to me

@samuelklee samuelklee merged commit 01c8445 into master Apr 4, 2018
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@samuelklee samuelklee deleted the sl_median_pct branch Apr 4, 2018
cwhelan added a commit to cwhelan/gatk-linked-reads that referenced this pull request May 25, 2018
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