Merge pull request #1167 from broadinstitute/rhl_bcbs
Implement BaseCounts per-sample
This commit is contained in:
Ron Levine
commit
e9724ebac7
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/*
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*/
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package org.broadinstitute.gatk.tools.walkers.annotator;
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import htsjdk.variant.variantcontext.Allele;
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import htsjdk.variant.variantcontext.Genotype;
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import htsjdk.variant.variantcontext.GenotypeBuilder;
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import htsjdk.variant.variantcontext.VariantContext;
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import htsjdk.variant.vcf.VCFFormatHeaderLine;
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import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
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import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation;
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import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
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import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
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import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele;
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import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
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import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
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import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
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import org.broadinstitute.gatk.utils.variant.GATKVCFConstants;
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import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines;
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import org.broadinstitute.gatk.utils.BaseUtils;
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import java.util.*;
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/**
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* Count of A, C, G, T bases for each sample
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*
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* <p> This annotation returns the counts of A, C, G, and T bases for each sample, in that order.</p>
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* <h3>Example:</h3>
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*
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* <pre>BCS=3,0,3,0</pre>
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*
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* <p>
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* This means the number of A bases seen is 3, the number of T bases seen is 0, the number of G bases seen is 3, and the number of T bases seen is 0.
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* </p>
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*
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* <p>
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* BaseCountsBySample is intended to provide insight into the pileup of bases used by HaplotypeCaller in the calling process, which may differ from the pileup
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* observed in the original bam file because of the local realignment and additional filtering performed internally by HaplotypeCaller.
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* </p>
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*
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* <h3>Caveats</h3>
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* <ul>
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* <li>Can only be requested from HaplotypeCaller, not VariantAnnotator.</li>
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* </ul>
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*
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* <h3>Related annotations</h3>
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* <ul>
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* <li><b><a href="https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_annotator_BaseCounts.php">BaseCounts</a></b> counts the percentage of N bases.</li>
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* </ul>
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*/
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public class BaseCountsBySample extends GenotypeAnnotation {
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@Override
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public void annotate(final RefMetaDataTracker tracker,
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final AnnotatorCompatible walker,
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final ReferenceContext ref,
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final AlignmentContext stratifiedContext,
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final VariantContext vc,
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final Genotype g,
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final GenotypeBuilder gb,
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final PerReadAlleleLikelihoodMap alleleLikelihoodMap) {
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if ( alleleLikelihoodMap != null && !alleleLikelihoodMap.isEmpty() )
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gb.attribute(GATKVCFConstants.BASE_COUNTS_BY_SAMPLE_KEY, getBaseCounts(alleleLikelihoodMap, vc));
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}
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@Override
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public List<String> getKeyNames() { return Collections.singletonList(GATKVCFConstants.BASE_COUNTS_BY_SAMPLE_KEY); }
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@Override
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public List<VCFFormatHeaderLine> getDescriptions() {
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return Collections.singletonList(GATKVCFHeaderLines.getFormatLine(getKeyNames().get(0)));
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}
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/**
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* Base counts given for the most likely allele
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*
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* @param perReadAlleleLikelihoodMap for each read, the underlying alleles represented by an aligned read, and corresponding relative likelihood.
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* @param vc variant context
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* @return count of A, C, G, T bases
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* @throws IllegalStateException if alleles in vc are not in perReadAlleleLikelihoodMap
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*/
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private int[] getBaseCounts(final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap, final VariantContext vc) {
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final Set<Allele> alleles = new HashSet<>(vc.getAlleles());
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// make sure that there's a meaningful relationship between the alleles in the perReadAlleleLikelihoodMap and our VariantContext
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if ( !perReadAlleleLikelihoodMap.getAllelesSet().containsAll(alleles) )
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throw new IllegalStateException("VC alleles " + alleles + " not a strict subset of per read allele map alleles " + perReadAlleleLikelihoodMap.getAllelesSet());
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final int[] counts = new int[4];
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for ( final Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : perReadAlleleLikelihoodMap.getLikelihoodReadMap().entrySet()) {
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final MostLikelyAllele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue(), alleles);
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if (! a.isInformative() ) continue; // read is non-informative
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for (final byte base : el.getKey().getReadBases() ){
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int index = BaseUtils.simpleBaseToBaseIndex(base);
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if ( index != -1 )
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counts[index]++;
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}
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}
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return counts;
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}
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}
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@ -74,7 +74,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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final static String REF = b37KGReference;
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final static String CEUTRIO_BAM = validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam";
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final static String standardAnnotations = " -G Standard -G StandardUG ";
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final static String STANDARD_ANNOTATIONS = " -G Standard -G StandardUG ";
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public static String baseTestString() {
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return "-T VariantAnnotator -R " + b36KGReference + " --no_cmdline_in_header -o %s";
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@ -99,7 +99,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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@Test
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public void testHasAnnotsAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("d6cd81fc2f483f29d44fbb27d1772841"));
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executeTest("test file has annotations, asking for annotations, #1", spec);
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}
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@ -107,7 +107,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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@Test
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public void testHasAnnotsAsking2() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
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baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
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Arrays.asList("300836de4e2c8424734d2ee0ca4261c1"));
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executeTest("test file has annotations, asking for annotations, #2", spec);
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}
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@ -133,7 +133,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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@Test
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public void testNoAnnotsAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("192f393da4e28aecf16112562e65083a"));
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executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
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}
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@ -141,7 +141,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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@Test
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public void testNoAnnotsAsking2() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
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baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
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Arrays.asList("52baff55535f7c87545a7818052a2d5c"));
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executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
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}
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@ -149,21 +149,21 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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@Test
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public void testExcludeAnnotations() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + standardAnnotations + "-XA FisherStrand -XA ReadPosRankSumTest --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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baseTestString() + STANDARD_ANNOTATIONS + "-XA FisherStrand -XA ReadPosRankSumTest --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("334915d90fa92ee9fa07d4647912ceac"));
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executeTest("test exclude annotations", spec);
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}
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@Test
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public void testAskingStrandAlleleCountsBySample() throws IOException{
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String logFileName = new String("testAskingStrandAlleleCountsBySample.log");
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File logFile = createTempFile("testAskingStrandAlleleCountsBySample.log", ".tmp");
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000 -A StrandAlleleCountsBySample -log " + logFileName, 1,
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baseTestString() + " --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000 "
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+ "-A StrandAlleleCountsBySample -log " + logFile.getAbsolutePath(), 1,
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Arrays.asList("5c0fe344544a887acbb5cd83083d303b"));
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executeTest("test file has annotations, adding StrandAlleleCountsBySample annotation", spec);
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File file = new File(logFileName);
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Assert.assertTrue(FileUtils.readFileToString(file).contains(AnnotationUtils.ANNOTATION_HC_WARN_MSG));
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Assert.assertTrue(FileUtils.readFileToString(logFile).contains(AnnotationUtils.ANNOTATION_HC_WARN_MSG));
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}
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@Test
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@ -182,7 +182,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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@Test
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public void testOverwritingHeader() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
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baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
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Arrays.asList("ab84654ac412a0aaaec99e86e357f0fd"));
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executeTest("test overwriting header", spec);
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}
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@ -190,7 +190,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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@Test
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public void testNoReads() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
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baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
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Arrays.asList("489a09a8531d9c8ef683ad8cc81db3e8"));
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executeTest("not passing it any reads", spec);
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}
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@ -198,7 +198,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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@Test
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public void testDBTagWithDbsnp() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --dbsnp " + b36dbSNP129 + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
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baseTestString() + " --dbsnp " + b36dbSNP129 + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
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Arrays.asList("a7af6774ea1f7622d999cae1b7f8ea32"));
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executeTest("getting DB tag with dbSNP", spec);
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}
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@ -206,7 +206,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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@Test
|
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public void testMultipleIdsWithDbsnp() {
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WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " --alwaysAppendDbsnpId --dbsnp " + b36dbSNP129 + standardAnnotations + "--variant " + privateTestDir + "vcfexample3withIDs.vcf -L " + privateTestDir + "vcfexample3withIDs.vcf", 1,
|
||||
baseTestString() + " --alwaysAppendDbsnpId --dbsnp " + b36dbSNP129 + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3withIDs.vcf -L " + privateTestDir + "vcfexample3withIDs.vcf", 1,
|
||||
Arrays.asList("de8cfffe3b61b7c8832096a399e9d954"));
|
||||
executeTest("adding multiple IDs with dbSNP", spec);
|
||||
}
|
||||
|
|
@ -214,7 +214,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testDBTagWithHapMap() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf" + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
|
||||
baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
|
||||
Arrays.asList("25443af7099f7de184b8dcdfb659f62e"));
|
||||
executeTest("getting DB tag with HM3", spec);
|
||||
}
|
||||
|
|
@ -222,7 +222,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testDBTagWithTwoComps() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf --comp:foo " + privateTestDir + "fakeHM3.vcf " + standardAnnotations + " --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
|
||||
baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf --comp:foo " + privateTestDir + "fakeHM3.vcf " + STANDARD_ANNOTATIONS + " --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
|
||||
Arrays.asList("ea9b10d2b82a7846c01a017f6f3bb57e"));
|
||||
executeTest("getting DB tag with 2 comps", spec);
|
||||
}
|
||||
|
|
@ -238,7 +238,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testUsingExpression() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf" + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty.vcf", 1,
|
||||
baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty.vcf", 1,
|
||||
Arrays.asList("f26d1f849cceca0ab115737f8db670ae"));
|
||||
executeTest("using expression", spec);
|
||||
}
|
||||
|
|
@ -246,7 +246,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testUsingExpressionMultiAllele() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations-multiAllele.vcf" + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty-multiAllele.vcf -E foo.AF -E foo.AC -L " + privateTestDir + "vcfexample3empty-multiAllele.vcf", 1,
|
||||
baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations-multiAllele.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty-multiAllele.vcf -E foo.AF -E foo.AC -L " + privateTestDir + "vcfexample3empty-multiAllele.vcf", 1,
|
||||
Arrays.asList("04280ba5accc0479c627c16902e54dd7"));
|
||||
executeTest("using expression with multi-alleles", spec);
|
||||
}
|
||||
|
|
@ -254,7 +254,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testUsingExpressionWithID() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf" + standardAnnotations + "--variant " + privateTestDir + "vcfexample3empty.vcf -E foo.ID -L " + privateTestDir + "vcfexample3empty.vcf", 1,
|
||||
baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -E foo.ID -L " + privateTestDir + "vcfexample3empty.vcf", 1,
|
||||
Arrays.asList("58a86fe8a34c92127eb33e36107941dd"));
|
||||
executeTest("using expression with ID", spec);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -452,7 +452,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
" -R " + REF +
|
||||
" -I " + NA12878_BAM +
|
||||
" -L " + INTERVALS_FILE +
|
||||
" --mergeVariantsViaLD " +
|
||||
" --mergeVariantsViaLD " +
|
||||
" -o %s",
|
||||
1, UserException.DeprecatedArgument.class));
|
||||
}
|
||||
|
|
@ -461,5 +461,10 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
public void testHaplotypeCallerTandemRepeatAnnotator() throws IOException{
|
||||
HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "2c108ecdc73e1158310dcdab1abf3e66");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testHBaseCountsBySample() throws IOException{
|
||||
HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A BaseCountsBySample", "f55b64e7457ed40dc8d56c499de9d516");
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -112,6 +112,7 @@ public final class GATKVCFConstants {
|
|||
//FORMAT keys
|
||||
public static final String ALLELE_BALANCE_KEY = "AB";
|
||||
public static final String ALLELE_FRACTION_KEY = "AF"; //M2
|
||||
public static final String BASE_COUNTS_BY_SAMPLE_KEY = "BCS";
|
||||
public static final String PL_FOR_ALL_SNP_ALLELES_KEY = "APL";
|
||||
public static final String RBP_HAPLOTYPE_KEY = "HP"; //ReadBackedPhasing
|
||||
public static final String AVG_INTERVAL_DP_BY_SAMPLE_KEY = "IDP"; //DiagnoseTargets
|
||||
|
|
|
|||
|
|
@ -73,6 +73,7 @@ public class GATKVCFHeaderLines {
|
|||
addFilterLine(new VCFFilterHeaderLine(GATKVCFConstants.TRIALLELIC_SITE_FILTER_NAME, "Site filtered because more than two alt alleles pass tumor LOD"));
|
||||
|
||||
addFormatLine(new VCFFormatHeaderLine(ALLELE_BALANCE_KEY, 1, VCFHeaderLineType.Float, "Allele balance for each het genotype"));
|
||||
addFormatLine(new VCFFormatHeaderLine(BASE_COUNTS_BY_SAMPLE_KEY, 4, VCFHeaderLineType.Integer, "Counts of each base by sample"));
|
||||
addFormatLine(new VCFFormatHeaderLine(MAPPING_QUALITY_ZERO_BY_SAMPLE_KEY, 1, VCFHeaderLineType.Integer, "Number of Mapping Quality Zero Reads per sample"));
|
||||
addFormatLine(new VCFFormatHeaderLine(MLE_PER_SAMPLE_ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Maximum likelihood expectation (MLE) for the alternate allele count, in the same order as listed, for each individual sample"));
|
||||
addFormatLine(new VCFFormatHeaderLine(MLE_PER_SAMPLE_ALLELE_FRACTION_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Maximum likelihood expectation (MLE) for the alternate allele fraction, in the same order as listed, for each individual sample"));
|
||||
|
|
|
|||
Loading…
Reference in New Issue