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Possible bug in Mutect2Engine.java #6901

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DonFreed opened this issue Oct 19, 2020 · 1 comment · Fixed by #6908
Closed
2 tasks done

Possible bug in Mutect2Engine.java #6901

DonFreed opened this issue Oct 19, 2020 · 1 comment · Fixed by #6908
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@davidbenjamin @fleharty
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Mutect

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@DonFreed
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Bug Report

Affected tool

Mutect2

Affected version(s)

  • Latest public release version 4.1.9.0
  • Latest master branch as of 10/19/2020

Description

It looks like there may be a typo in Mutect2Engine.java that was introduced before the most recent release, https://github.com/broadinstitute/gatk/blob/master/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java#L392

The line currently reads:

if (bestNormalAltAllele.getLeft() == bestNormalAltAllele.getLeft()) {

It seems like this line should instead be:

if (bestNormalAltAllele.getLeft() == bestTumorAltAllele.getLeft()) {
@droazen droazen added the Mutect label Oct 20, 2020
@droazen droazen changed the title Possible typo in Mutect2Engine.java Possible bug in Mutect2Engine.java Oct 20, 2020
@davidbenjamin davidbenjamin mentioned this issue Oct 23, 2020
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@DonFreed
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Thanks!

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@davidbenjamin davidbenjamin

@fleharty fleharty

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fix bug in M2 engine active region code broadinstitute/gatk
4 participants
@droazen @DonFreed @davidbenjamin @fleharty