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Trim per-allele FORMAT annotations and optionally retain raw AS annotations #5833
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@nh3 care to take a look? In the GGVCFs integration test, the with OxoGReadCounts.g.vcf file has
with read counts
after genotyping alleles get dropped and trimmed and we have
Do you agree that's as expected? (I couldn't reproduce your exact example without the exact bam.) |
Also @tfenne hopefully this meets expectations for AS_SB_TABLE (which I have now added in AS_Annotations.keepRawCombined.expected.vcf) |
Codecov Report
@@ Coverage Diff @@
## master #5833 +/- ##
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- Coverage 87.041% 36.071% -50.971%
+ Complexity 32151 17630 -14521
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Files 1974 1977 +3
Lines 147413 147117 -296
Branches 16225 16181 -44
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- Hits 128310 53066 -75244
- Misses 13185 89228 +76043
+ Partials 5918 4823 -1095
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I believe this was meant for @nh13, not me. |
Sorry. I don't think that's the only one. Bad case of the Mondays. |
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LGTM
src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java
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* If specified, keep the combined raw annotations (e.g. AS_SB_TABLE) after genotyping. This is applicable to Allele-Specific annotations | ||
*/ | ||
@Argument(fullName=KEEP_COMBINED_LONG_NAME, shortName = KEEP_COMBINED_SHORT_NAME, doc = "If specified, keep the combined raw annotations") | ||
protected boolean keepCombined = false; |
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Thanks @ldgauthier! This looks great.
Thanks again for getting this done and merged @ldgauthier & @droazen! |
GenotypeGVCFs now uses the header info to determine if FORMAT lists need to be subset when alleles are dropped. Fixes #5704
Added an option to keep raw AS values like AS_SB_TABLE and AS_QUAL, as requested in #5698 (does not close that issue)