Updating the FunctionalClass stratification in VariantEval to handle the snpEff annotations; this change really needs to be in before the release so that the pipeline can output semi-meaningful plots. This commit maintains backwards compatibility with the crappy Genomic Annotator output. However, I did clean up the code a bit so that we now use an Enum instead of hard-coded values (so it's now much easier to change things if we choose to do so in the future). I do not see this as the final commit on this topic - I think we need to make some changes to the snpEff annotator to preferentially choose certain annotations within effect classes; Mark, let's chat about this for a bit when you get back next week. Also, for the record, I should be blamed for David's temporary commit the other day because I gave him the green light (since when do you care about backwards compatibility anyways?). In any case, at least now we have something that works for both the old and new annotations.
This commit is contained in:
Eric Banks
parent
1e682deb26
commit
202405b1a1
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import java.util.ArrayList;
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@ -11,12 +12,19 @@ import java.util.List;
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* Stratifies by nonsense, missense, silent, and all annotations in the input ROD, from the INFO field annotation.
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*/
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public class FunctionalClass extends VariantStratifier {
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public enum FunctionalType {
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silent,
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missense,
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nonsense
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}
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@Override
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public void initialize() {
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states.add("all");
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states.add("silent");
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states.add("missense");
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states.add("nonsense");
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for ( FunctionalType type : FunctionalType.values() )
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states.add(type.name());
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}
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@ -26,10 +34,12 @@ public class FunctionalClass extends VariantStratifier {
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relevantStates.add("all");
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if (eval != null && eval.isVariant()) {
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String type = null;
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FunctionalType type = null;
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if (eval.hasAttribute("refseq.functionalClass")) {
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type = eval.getAttributeAsString("refseq.functionalClass");
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try {
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type = FunctionalType.valueOf(eval.getAttributeAsString("refseq.functionalClass"));
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} catch ( Exception e ) {} // don't error out if the type isn't supported
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} else if (eval.hasAttribute("refseq.functionalClass_1")) {
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int annotationId = 1;
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String key;
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@ -37,24 +47,33 @@ public class FunctionalClass extends VariantStratifier {
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do {
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key = String.format("refseq.functionalClass_%d", annotationId);
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String newtype = eval.getAttributeAsString(key);
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if ( newtype != null && !newtype.equalsIgnoreCase("null") &&
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( type == null ||
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( type.equals("silent") && !newtype.equals("silent") ) ||
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( type.equals("missense") && newtype.equals("nonsense") ) )
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) {
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type = newtype;
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String newtypeStr = eval.getAttributeAsString(key);
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if ( newtypeStr != null && !newtypeStr.equalsIgnoreCase("null") ) {
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try {
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FunctionalType newType = FunctionalType.valueOf(newtypeStr);
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if ( type == null ||
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( type == FunctionalType.silent && newType != FunctionalType.silent ) ||
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( type == FunctionalType.missense && newType == FunctionalType.nonsense ) ) {
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type = newType;
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}
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} catch ( Exception e ) {} // don't error out if the type isn't supported
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}
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annotationId++;
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} while (eval.hasAttribute(key));
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} else if ( eval.hasAttribute(SnpEff.InfoFieldKey.EFF.name() ) ) {
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SnpEff.EffectType snpEffType = SnpEff.EffectType.valueOf(eval.getAttribute(SnpEff.InfoFieldKey.EFF.name()).toString());
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if ( snpEffType == SnpEff.EffectType.STOP_GAINED )
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type = FunctionalType.nonsense;
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else if ( snpEffType == SnpEff.EffectType.NON_SYNONYMOUS_CODING )
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type = FunctionalType.missense;
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else if ( snpEffType == SnpEff.EffectType.SYNONYMOUS_CODING )
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type = FunctionalType.silent;
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}
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if (type != null) {
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if (type.equals("silent")) { relevantStates.add("silent"); }
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else if (type.equals("missense")) { relevantStates.add("missense"); }
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else if (type.equals("nonsense")) { relevantStates.add("nonsense"); }
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if ( type != null ) {
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relevantStates.add(type.name());
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}
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}
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@ -6,7 +6,7 @@ import org.testng.annotations.Test;
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import java.util.Arrays;
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public class VariantEvalIntegrationTest extends WalkerTest {
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private static String variantEvalTestDataRoot = validationDataLocation + "/VariantEval";
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private static String variantEvalTestDataRoot = validationDataLocation + "VariantEval";
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private static String fundamentalTestVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.snps_and_indels.vcf";
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private static String fundamentalTestSNPsVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.vcf";
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private static String fundamentalTestSNPsOneSampleVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.HG00625.vcf";
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@ -14,6 +14,27 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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private static String cmdRoot = "-T VariantEval" +
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" -R " + b36KGReference;
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@Test
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public void testFunctionClassWithSnpeff() {
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WalkerTestSpec spec = new WalkerTestSpec(
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buildCommandLine(
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"-T VariantEval",
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"-R " + b37KGReference,
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"--dbsnp " + b37dbSNP132,
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"--eval " + validationDataLocation + "snpEff.AFR.unfiltered.VariantAnnotator.output.vcf",
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"-noEV",
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"-EV TiTvVariantEvaluator",
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"-noST",
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"-ST FunctionalClass",
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"-BTI eval",
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"-o %s"
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),
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1,
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Arrays.asList("f5f811ceb973d7fd6c1b2b734f1b2b12")
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);
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executeTest("testStratifySamplesAndExcludeMonomorphicSites", spec);
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}
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@Test
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public void testStratifySamplesAndExcludeMonomorphicSites() {
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WalkerTestSpec spec = new WalkerTestSpec(
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@ -21,7 +42,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-T VariantEval",
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"-R " + b37KGReference,
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"--dbsnp " + b37dbSNP132,
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"--eval " + variantEvalTestDataRoot + "/CEU.trio.callsForVE.vcf",
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"--eval " + variantEvalTestDataRoot + "CEU.trio.callsForVE.vcf",
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"-noEV",
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"-EV TiTvVariantEvaluator",
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"-ST Sample",
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