Adding TransmittedSingleton annotation and adding quality threshold a… #8329
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…rguments to PossibleDenovo Annotation
| @@ -111,4 +111,14 @@ void validateArguments(Collection<String> founderIds, GATKPath pedigreeFile) { | |||
| public @Nullable GATKPath getPedigreeFile() { | |||
| return pedigreeFile; | |||
| } | |||
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| protected boolean contextHasTrioGQs(final VariantContext vc, final Trio trio) { | |||
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Add a descriptive comment to this method.
| final Genotype g11gq45 = new GenotypeBuilder("3", homVar).DP(50).PL(new int[]{100, 100, 0}).AD(new int[]{0, 10}).GQ(GQ45).make(); | ||
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| tests.add(new Object[]{g00gq45, g00gq45, g00gq45, false, false}); | ||
| tests.add(new Object[]{g00gq45, g00gq45, g01gq45, false, true}); |
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only one positive case for this second condition? A quick inline comment explaining these extra tests would be helpful.
| @@ -53,6 +53,8 @@ public final class GATKVCFConstants { | |||
| public static final String GQ_STDEV_KEY = "GQ_STDDEV"; | |||
| public static final String HAPLOTYPE_SCORE_KEY = "HaplotypeScore"; | |||
| public static final String HI_CONF_DENOVO_KEY = "hiConfDeNovo"; | |||
| public static final String TRANSMITTED_SINGLETON = "transmittedSingleton"; | |||
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Generally these are captialized... i don't know if this breaks already run samples however...
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I was trying to follow the PossibleDeNovo convention which has hiConfDeNovo and loConfDeNovo. Those have been in production a long time (unlike transmittedSingleton), so I'm hesitant to change them. What do you think?
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This is low priority and you know better than i do. Feel free to ignore this comment I you like.
| childIsHighGQHet && oneParentHasAllele && momIsHighGQ && dadIsHighGQ) { | ||
| transmittedSingletonParent.add(matchingParentId); | ||
| } | ||
| //TODO: This only works for trios (not quads or other more complicated family structures that would effect number of singletons for parents or transmission to multiple kids) |
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what happens if the pedigree file has 2 kids in it? Will this clobber one/another? Should we add some defensive behavior to make sure this doesn't break anything?
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We have lots of singleton loggers putting warnings out about annotation warnings like this. IF you wanted to add a "detected a quad pedigree this will cause xyz problems" and we should probably at least have some tests codifying the behavior.
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I made this all clearer and added a warning and a test.
| tests.add(new Object[]{g00NoPl, g00NoPl, g01NoPl, false, false, null}); | ||
| tests.add(new Object[]{g00NoPl, g01NoPl, g01NoPl, true, false, DAD}); | ||
| tests.add(new Object[]{g00NoPl, g01NoPl, g00NoPl, false, true, DAD}); | ||
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can you add some tests documenting exactly what falls over when you have quads?
| @@ -39,11 +40,24 @@ public final class PossibleDeNovo extends PedigreeAnnotation implements InfoFiel | |||
| private final MendelianViolation mendelianViolation; | |||
| private Set<Trio> trios; | |||
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| @Argument(fullName = "denovo-parent-gq-threshold", doc = "Minimum genotype quality for parents to be considered for de novo calculation (separate from GQ thershold for full trio).", optional = true) | |||
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Now that we have these new arguments can you add a test into the GATKAnnotationPluginDescriptorUnitTest to be really certain that this machinery works reasonably well with the pedigree file + these extra arguments? Sorry to ask this of you but we don't have a lot of examples of annotation arguments and I want to be sure it really works in the engine as expected.
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I tried to add this test, but please take a look and make sure it's doing what you expected.
…rguments to PossibleDenovo Annotation
@jamesemery, could you please review this (or suggest someone)? This adds annotations that we used in an analysis for @ilyasoifer awhile back that we'd like to be reproducible for other users.