handle unmarked duplicates with mate MQ = 0 in Mutect2 #5734
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Codecov Report
@@ Coverage Diff @@
## master #5734 +/- ##
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+ Coverage 87.061% 87.071% +0.01%
- Complexity 31880 31902 +22
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Files 1940 1940
Lines 146804 146832 +28
Branches 16234 16238 +4
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+ Hits 127809 127848 +39
+ Misses 13073 13064 -9
+ Partials 5922 5920 -2
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@davidbenjamin Results on FC looked really good. Reviewed manually. |
LeeTL1220
approved these changes
Feb 28, 2019
| assemblyRegion.removeAll(readStubs); | ||
| } | ||
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| private void removeUnmarkedDuplicates(final AssemblyRegion assemblyRegion) { |
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This looks like it considers:
- SVs: This code checks whether the mates are clustered, even if on a different contig from the supporting reads of the variant.
- Duplicate start and end positions of supporting reads.
Please tell me if I have misinterpreted. If I have not misinterpreted, then no action required.
| @@ -1150,4 +1150,20 @@ private static String keyForVariant( final VariantContext variant ) { | |||
| return String.format("%s:%d-%d %s, %s", variant.getContig(), variant.getStart(), variant.getEnd(), variant.getReference(), | |||
| variant.getAlternateAlleles().stream().map(Allele::getDisplayString).sorted().collect(Collectors.toList())); | |||
| } | |||
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| @Test | |||
| public void testSachet() throws Exception { | |||
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Can we rename to something about missed duplicates? And if you want to thank Sachet in a comment, that should be okay.
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@davidbenjamin Back to you |
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@LeeTL1220 This is for Sachet's artifact, ready to review pending the results on Firecloud looking good.