Adding dbsnp annotation back into the UG integration tests
This commit is contained in:
Ryan Poplin
parent
b705d9cf15
commit
902eb0c61e
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@ -16,8 +16,8 @@ import java.util.Map;
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public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm BOTH";
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private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm INDEL";
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private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm BOTH --dbsnp " + b36dbSNP129;
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private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm INDEL --dbsnp " + b36dbSNP129;
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// --------------------------------------------------------------------------------------------------------------
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//
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@ -28,7 +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("16b0c7b47745abcd1ddaa2e261719530"));
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Arrays.asList("149e6ad9b3fd23551254a691286a96b3"));
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executeTest("test MultiSample Pilot1", spec);
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}
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@ -54,12 +54,12 @@ 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("811ddc0bd8322b14f14f58df8c627aa9"));
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Arrays.asList("8de2602679ffc92388da0b6cb4325ef6"));
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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("5cf08dd7ac3d218082f7be3915ce0b15"));
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Arrays.asList("ec43daadfb15b00b41aeb0017a45df0b"));
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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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@ -67,7 +67,7 @@ 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("75156264696563c2f47620fef9424f7c"));
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Arrays.asList("82d469145c174486ccc494884852cc58"));
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executeTest("test SingleSample Pilot2", spec);
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}
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@ -77,7 +77,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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//
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// --------------------------------------------------------------------------------------------------------------
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private final static String COMPRESSED_OUTPUT_MD5 = "7255e03430549cb97d8fcae34cbffb02";
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private final static String COMPRESSED_OUTPUT_MD5 = "a5a9f38c645d6004d4640765a8b77ce4";
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@Test
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public void testCompressedOutput() {
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@ -107,7 +107,7 @@ 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 = "7912109e83fda21dae90ef8d5dd0140d";
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String md5 = "0a45761c0e557d9c2080eb9e7f4f6c41";
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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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@ -138,10 +138,9 @@ 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", "6d3aa9f783ca63f37c952f83eeda593c" );
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e.put( "--min_mapping_quality_score 26", "51bfdf777123bf49de5d92ffde5c74e7" );
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e.put( "--p_nonref_model GRID_SEARCH", "333328ab2c8da2875fade599e80a271f" );
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e.put( "--computeSLOD", "226caa28a4fa9fe34f3beb8a23f3d53d" );
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e.put( "--min_base_quality_score 26", "531966aee1cd5dced61c96c4fedb59a9" );
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e.put( "--min_mapping_quality_score 26", "c71ca370947739cb7d87b59452be7a07" );
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e.put( "--computeSLOD", "1a5648f26c18ced27df4be031b44e72d" );
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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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@ -154,9 +153,9 @@ 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", "5f659dee408710d3709ed72005cd863a" );
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e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "55d09bf13149bddc06cc36be0801507b" );
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e.put( "--output_mode EMIT_ALL_SITES", "727f49dcb2439b18446829efc3b1561c" );
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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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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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@ -170,12 +169,12 @@ 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("51bfdf777123bf49de5d92ffde5c74e7"));
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Arrays.asList("c71ca370947739cb7d87b59452be7a07"));
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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("c67c285e70fd4457c9f9ce7bd878ddca"));
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Arrays.asList("1c0a599d475cc7d5e745df6e9b6c0d29"));
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executeTest("test confidence 2", spec2);
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}
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@ -187,8 +186,8 @@ 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, "7ecc564d4db97d5932cef2e558550ed2" );
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e.put( 1.0 / 1850, "aa9e101bb9f9e111fe292fec467d915a" );
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e.put( 0.01, "af5199fbc0853cf5888acdcc88f012bc" );
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e.put( 1.0 / 1850, "4e6938645ccde1fdf204ffbf4e88170f" );
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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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@ -212,7 +211,7 @@ 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("2efd686186b2c5129be4cf89274a24dd"));
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Arrays.asList("213ebaaaacf850312d885e918eb33500"));
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executeTest(String.format("test multiple technologies"), spec);
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}
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@ -231,7 +230,7 @@ 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("2892d35331fe9fc141ba19269ec7caed"));
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Arrays.asList("3aecba34a89f3525afa57a38dc20e6cd"));
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executeTest(String.format("test calling with BAQ"), spec);
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}
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@ -250,7 +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("8c2afb4289ed44521933d1a74c8d6c7f"));
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Arrays.asList("043973c719a85de29a35a33a674616fb"));
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executeTest(String.format("test indel caller in SLX"), spec);
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}
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@ -265,7 +264,7 @@ 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("b6fb70590a10e1c27fb611732916f27d"));
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Arrays.asList("68d4e6c1849e892467aed61c33e7bf24"));
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executeTest(String.format("test indel caller in SLX witn low min allele count"), spec);
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}
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@ -278,7 +277,7 @@ 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("61642502bd08cc03cdaaeb83a5426b46"));
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Arrays.asList("f86d453c5d2d2f33fb28ae2050658a5e"));
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executeTest(String.format("test indel calling, multiple technologies"), spec);
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}
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@ -288,14 +287,14 @@ 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("69b0b3f089c80b9864294d838a061336"));
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Arrays.asList("408d3aba4d094c067fc00a43992c2292"));
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executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1);
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WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
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baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
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+ 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("c90174cfd7dd68bdef36fe2c60145e10"));
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Arrays.asList("94977d6e42e764280e9deaf4e3ac8c80"));
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executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2);
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}
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