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Modified VariantEval FunctionalClass stratification to remove hardcoded GenomicAnnotator keynames 

This is a temporary and hopefully short-lived solution. I've modified
the FunctionalClass stratification to stratify by effect impact as
defined by SnpEff annotations (high, moderate, and low impact) rather
than by the silent/missense/nonsense categories.

If we want to bring back the silent/missense/nonsense stratification,
we should probably take the approach of asking the SnpEff author
to add it as a feature to SnpEff rather than coding it ourselves,
since the whole point of moving to SnpEff was to outsource genomic
annotation.
This commit is contained in:
David Roazen 2011-09-14 06:04:32 -04:00
parent 1213b2f8c6
commit e0c8c0ddcb
2 changed files with 24 additions and 36 deletions
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53
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
View File

@ -2,21 +2,29 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.ArrayList;
import java.util.List;
/**
* Stratifies by nonsense, missense, silent, and all annotations in the input ROD, from the INFO field annotation.
* Stratifies by low-, moderate-, and high-impact genomic effect using SnpEff annotations produced by VariantAnnotator
*/
public class FunctionalClass extends VariantStratifier {
public static final String LOW_IMPACT_STATE_NAME = "low-impact";
public static final String MODERATE_IMPACT_STATE_NAME = "moderate-impact";
public static final String HIGH_IMPACT_STATE_NAME = "high-impact";
public static final String EFFECT_IMPACT_ATTRIBUTE_KEY = SnpEff.InfoFieldKey.EFF_IMPACT.toString();
@Override
public void initialize() {
states.add("all");
states.add("silent");
states.add("missense");
states.add("nonsense");
states.add(LOW_IMPACT_STATE_NAME);
states.add(MODERATE_IMPACT_STATE_NAME);
states.add(HIGH_IMPACT_STATE_NAME);
}
@ -25,36 +33,17 @@ public class FunctionalClass extends VariantStratifier {
relevantStates.add("all");
if (eval != null && eval.isVariant()) {
String type = null;
if ( eval != null && eval.isVariant() && eval.hasAttribute(EFFECT_IMPACT_ATTRIBUTE_KEY) ) {
String effectImpact = eval.getAttributeAsString(EFFECT_IMPACT_ATTRIBUTE_KEY);
if (eval.hasAttribute("refseq.functionalClass")) {
type = eval.getAttributeAsString("refseq.functionalClass");
} else if (eval.hasAttribute("refseq.functionalClass_1")) {
int annotationId = 1;
String key;
do {
key = String.format("refseq.functionalClass_%d", annotationId);
String newtype = eval.getAttributeAsString(key);
if ( newtype != null && !newtype.equalsIgnoreCase("null") &&
( type == null ||
( type.equals("silent") && !newtype.equals("silent") ) ||
( type.equals("missense") && newtype.equals("nonsense") ) )
) {
type = newtype;
}
annotationId++;
} while (eval.hasAttribute(key));
if ( effectImpact.equals(SnpEff.EffectImpact.LOW.toString()) ) {
relevantStates.add(LOW_IMPACT_STATE_NAME);
}
if (type != null) {
if (type.equals("silent")) { relevantStates.add("silent"); }
else if (type.equals("missense")) { relevantStates.add("missense"); }
else if (type.equals("nonsense")) { relevantStates.add("nonsense"); }
else if ( effectImpact.equals(SnpEff.EffectImpact.MODERATE.toString()) ) {
relevantStates.add(MODERATE_IMPACT_STATE_NAME);
}
else if ( effectImpact.equals(SnpEff.EffectImpact.HIGH.toString()) ) {
relevantStates.add(HIGH_IMPACT_STATE_NAME);
}
}

7
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -123,9 +123,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"--dbsnp " + b37dbSNP132,
"--eval " + fundamentalTestVCF,
"-R " + hg19Reference,
"--eval " + validationDataLocation + "snpEff.AFR.unfiltered.VariantAnnotator.output.vcf",
"-noEV",
"-EV CountVariants",
"-noST",
@ -134,7 +133,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("e40b77e7ed6581328e373a24b93cd170")
Arrays.asList("e93b3d66a5c150cbf1ae4262ec075d2d")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithFunctionalClass", spec);
}