Updated header description for the INFO and FORMAT DP fields to be more accurate.
This commit is contained in:
Eric Banks
parent
e7d41d8d33
commit
16a021992b
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@ -49,5 +49,5 @@ public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnno
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public List<String> getKeyNames() { return Arrays.asList(VCFConstants.DEPTH_KEY); }
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public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Integer, "Filtered Depth")); }
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public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Integer, "Approximate read depth; some reads may have been filtered")); }
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}
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@ -258,7 +258,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
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Set<VCFFormatHeaderLine> result = new HashSet<VCFFormatHeaderLine>();
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result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
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result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Genotype Quality"));
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result.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Read Depth (only filtered reads used for calling)"));
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result.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Approximate read depth (reads with MQ=255 or with bad mates are filtered)"));
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result.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"));
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return result;
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@ -32,7 +32,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testHasAnnotsAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "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("8e7de435105499cd71ffc099e268a83e"));
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Arrays.asList("9beb795536e95954f810835c6058f2ad"));
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executeTest("test file has annotations, asking for annotations, #1", spec);
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}
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@ -40,7 +40,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testHasAnnotsAsking2() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "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("64b6804cb1e27826e3a47089349be581"));
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Arrays.asList("2977bb30c8b84a5f4094fe6090658561"));
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executeTest("test file has annotations, asking for annotations, #2", spec);
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}
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@ -64,7 +64,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testNoAnnotsAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "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("fd1ffb669800c2e07df1e2719aa38e49"));
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Arrays.asList("49d989f467b8d6d8f98f7c1b67cd4a05"));
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executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
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}
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@ -72,7 +72,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testNoAnnotsAsking2() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "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("09f8e840770a9411ff77508e0ed0837f"));
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Arrays.asList("0948cd1dba7d61f283cc4cf2a7757d92"));
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executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
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}
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@ -80,7 +80,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testExcludeAnnotations() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant:VCF3 " + validationDataLocation + "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("b49fe03aa4b675db80a9db38a3552c95"));
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Arrays.asList("33062eccd6eb73bc49440365430454c4"));
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executeTest("test exclude annotations", spec);
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}
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@ -88,7 +88,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testOverwritingHeader() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant " + validationDataLocation + "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("78d2c19f8107d865970dbaf3e12edd92"));
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Arrays.asList("062155edec46a8c52243475fbf3a2943"));
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executeTest("test overwriting header", spec);
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}
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@ -96,7 +96,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testNoReads() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant " + validationDataLocation + "vcfexample3empty.vcf -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
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Arrays.asList("16e3a1403fc376320d7c69492cad9345"));
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Arrays.asList("06635f2dd91b539bfbce9bf7914d8e43"));
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executeTest("not passing it any reads", spec);
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}
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@ -104,7 +104,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testDBTagWithDbsnp() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --dbsnp " + b36dbSNP129 + " -G Standard --variant " + validationDataLocation + "vcfexample3empty.vcf -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
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Arrays.asList("3da8ca2b6bdaf6e92d94a8c77a71313d"));
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Arrays.asList("820eeba1f6e3a0758a69d937c524a38e"));
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executeTest("getting DB tag with dbSNP", spec);
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}
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@ -112,7 +112,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testDBTagWithHapMap() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --comp:H3 " + validationDataLocation + "fakeHM3.vcf -G Standard --variant " + validationDataLocation + "vcfexample3empty.vcf -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
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Arrays.asList("1bc01c5b3bd0b7aef75230310c3ce688"));
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Arrays.asList("31cc2ce157dd20771418c08d6b3be1fa"));
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executeTest("getting DB tag with HM3", spec);
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}
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@ -120,7 +120,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testUsingExpression() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --resource:foo " + validationDataLocation + "targetAnnotations.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
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Arrays.asList("ae30a1ac7bfbc3d22a327f8b689cad31"));
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Arrays.asList("074865f8f8c0ca7bfd58681f396c49e9"));
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executeTest("using expression", spec);
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}
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@ -128,7 +128,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testUsingExpressionWithID() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --resource:foo " + validationDataLocation + "targetAnnotations.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.ID -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
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Arrays.asList("1b4921085b26cbfe07d53b7c947de1e5"));
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Arrays.asList("97b26db8135d083566fb585a677fbe8a"));
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executeTest("using expression with ID", spec);
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}
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@ -5,10 +5,8 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.testng.annotations.Test;
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import java.io.File;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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// ********************************************************************************** //
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@ -30,7 +28,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMultiSamplePilot1() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
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Arrays.asList("b27939251539439a382538e507e03507"));
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Arrays.asList("364a6112e6034571a896d4c68b6ff02a"));
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executeTest("test MultiSample Pilot1", spec);
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}
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@ -38,12 +36,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testWithAllelesPassedIn() {
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WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
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baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
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Arrays.asList("8de2602679ffc92388da0b6cb4325ef6"));
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Arrays.asList("6cce55734ecd1a56c33f0ecba67d1258"));
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executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
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WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
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baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
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Arrays.asList("6458f3b8fe4954e2ffc2af972aaab19e"));
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Arrays.asList("b2a00130a4b6f9a3c31288a236f5d159"));
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executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
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}
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@ -51,7 +49,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testSingleSamplePilot2() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
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Arrays.asList("6762b72ae60155ad71738d7c76b80e4b"));
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Arrays.asList("3ccce5d909f8f128e496f6841836e5f7"));
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executeTest("test SingleSample Pilot2", spec);
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}
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@ -61,7 +59,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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//
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// --------------------------------------------------------------------------------------------------------------
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private final static String COMPRESSED_OUTPUT_MD5 = "bc71dba7bbdb23e7d5cc60461fdd897b";
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private final static String COMPRESSED_OUTPUT_MD5 = "890143b366050e78d6c6ba6b2c6b6864";
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@Test
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public void testCompressedOutput() {
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@ -82,7 +80,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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// Note that we need to turn off any randomization for this to work, so no downsampling and no annotations
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String md5 = "b9504e446b9313559c3ed97add7e8dc1";
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String md5 = "95614280c565ad90f8c000376fef822c";
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WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
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baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
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@ -113,8 +111,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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@Test
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public void testCallingParameters() {
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HashMap<String, String> e = new HashMap<String, String>();
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e.put( "--min_base_quality_score 26", "bb3f294eab3e2cf52c70e63b23aac5ee" );
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e.put( "--computeSLOD", "eb34979efaadba1e34bd82bcacf5c722" );
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e.put( "--min_base_quality_score 26", "7acb1a5aee5fdadb0cc0ea07a212efc6" );
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e.put( "--computeSLOD", "e9d23a08472e4e27b4f25e844f5bad57" );
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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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@ -127,9 +125,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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@Test
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public void testOutputParameter() {
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HashMap<String, String> e = new HashMap<String, String>();
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e.put( "-sites_only", "d40114aa201aa33ff5f174f15b6b73af" );
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e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "3c681b053fd2280f3c42041d24243752" );
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e.put( "--output_mode EMIT_ALL_SITES", "eafa6d71c5ecd64dfee5d7a3f60e392e" );
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e.put( "-sites_only", "44f3b5b40e6ad44486cddfdb7e0bfcd8" );
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e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "94e53320f14c5ff29d62f68d36b46fcd" );
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e.put( "--output_mode EMIT_ALL_SITES", "73ad1cc41786b12c5f0e6f3e9ec2b728" );
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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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@ -143,12 +141,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testConfidence() {
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WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
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Arrays.asList("c71ca370947739cb7d87b59452be7a07"));
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Arrays.asList("902327e8a45fe585c8dfd1a7c4fcf60f"));
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executeTest("test confidence 1", spec1);
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WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1,
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Arrays.asList("1c0a599d475cc7d5e745df6e9b6c0d29"));
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Arrays.asList("9ef66764a0ecfe89c3e4e1a93a69e349"));
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executeTest("test confidence 2", spec2);
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}
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@ -160,8 +158,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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@Test
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public void testHeterozyosity() {
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HashMap<Double, String> e = new HashMap<Double, String>();
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e.put( 0.01, "f84da90c310367bd51f2ab6e346fa3d8" );
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e.put( 1.0 / 1850, "5791e7fef40d4412b6d8f84e0a809c6c" );
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e.put( 0.01, "46243ecc2b9dc716f48ea280c9bb7e72" );
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e.put( 1.0 / 1850, "6b2a59dbc76984db6d4d6d6b5ee5d62c" );
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for ( Map.Entry<Double, String> entry : e.entrySet() ) {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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@ -185,7 +183,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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" -o %s" +
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" -L 1:10,000,000-10,100,000",
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1,
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Arrays.asList("9cc9538ac83770e12bd0830d285bfbd0"));
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Arrays.asList("f0fbe472f155baf594b1eeb58166edef"));
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executeTest(String.format("test multiple technologies"), spec);
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}
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@ -204,7 +202,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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" -L 1:10,000,000-10,100,000" +
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" -baq CALCULATE_AS_NECESSARY",
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1,
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Arrays.asList("eaf8043edb46dfbe9f97ae03baa797ed"));
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Arrays.asList("8c87c749a7bb5a76ed8504d4ec254272"));
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executeTest(String.format("test calling with BAQ"), spec);
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}
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@ -223,7 +221,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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" -o %s" +
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" -L 1:10,000,000-10,500,000",
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1,
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Arrays.asList("eeba568272f9b42d5450da75c7cc6d2d"));
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Arrays.asList("a64d2e65b5927260e4ce0d948760cc5c"));
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executeTest(String.format("test indel caller in SLX"), spec);
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}
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@ -238,7 +236,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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" -minIndelCnt 1" +
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" -L 1:10,000,000-10,100,000",
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1,
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Arrays.asList("5fe98ee853586dc9db58f0bc97daea63"));
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Arrays.asList("2ad52c2e75b3ffbfd8f03237c444e8e6"));
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executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
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}
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@ -251,7 +249,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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" -o %s" +
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" -L 1:10,000,000-10,500,000",
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1,
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Arrays.asList("19ff9bd3139480bdf79dcbf117cf2b24"));
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Arrays.asList("69107157632714150fc068d412e31939"));
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executeTest(String.format("test indel calling, multiple technologies"), spec);
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}
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@ -261,7 +259,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
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baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
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"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
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Arrays.asList("118918f2e9e56a3cfc5ccb2856d529c8"));
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Arrays.asList("84f065e115004e4c9d9d62f1bf6b4f44"));
|
||||
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1);
|
||||
}
|
||||
|
||||
|
|
@ -271,7 +269,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
|
||||
+ validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
|
||||
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
|
||||
Arrays.asList("a20799237accd52c1b8c2ac096309c8f"));
|
||||
Arrays.asList("7ea8372e4074f90ec942f964e1863351"));
|
||||
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2);
|
||||
}
|
||||
|
||||
|
|
@ -281,7 +279,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
|
||||
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2.20101123.indels.sites.vcf -I " + validationDataLocation +
|
||||
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,080,000", 1,
|
||||
Arrays.asList("18ef8181157b4ac3eb8492f538467f92"));
|
||||
Arrays.asList("94afa8c011b47af7323c821bf19106b4"));
|
||||
executeTest("test MultiSample Pilot2 indels with complicated records", spec3);
|
||||
}
|
||||
|
||||
|
|
@ -290,7 +288,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
WalkerTest.WalkerTestSpec spec4 = new WalkerTest.WalkerTestSpec(
|
||||
baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2_chr20_100_110K.20101123.indels.sites.vcf -I " + validationDataLocation +
|
||||
"phase1_GBR_realigned.chr20.100K-110K.bam -o %s -L 20:100,000-110,000", 1,
|
||||
Arrays.asList("ad884e511a751b05e64db5314314365a"));
|
||||
Arrays.asList("1e02f57fafaa41db71c531eb25e148e1"));
|
||||
executeTest("test MultiSample 1000G Phase1 indels with complicated records emitting all sites", spec4);
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue