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Merge pull request #174 from broadinstitute/md_hc_parameters 

Two sensitivity / specificity improvements to the haplotype caller
This commit is contained in:
Ryan Poplin 2013-04-17 12:33:42 -07:00
parent b27706859a f0e64850da
commit ef8679c0a0
4 changed files with 13 additions and 13 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
View File

@ -845,7 +845,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
private List<GATKSAMRecord> filterNonPassingReads( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) {
final List<GATKSAMRecord> readsToRemove = new ArrayList<GATKSAMRecord>();
for( final GATKSAMRecord rec : activeRegion.getReads() ) {
if( rec.getReadLength() < 24 || rec.getMappingQuality() < 20 || BadMateFilter.hasBadMate(rec) || (keepRG != null && !rec.getReadGroup().getId().equals(keepRG)) ) {
if( rec.getReadLength() < 10 || rec.getMappingQuality() < 20 || BadMateFilter.hasBadMate(rec) || (keepRG != null && !rec.getReadGroup().getId().equals(keepRG)) ) {
readsToRemove.add(rec);
}
}

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java
View File

@ -60,7 +60,7 @@ import java.util.List;
* Date: Mar 14, 2011
*/
public abstract class LocalAssemblyEngine {
public static final byte DEFAULT_MIN_BASE_QUALITY_TO_USE = (byte) 16;
public static final byte DEFAULT_MIN_BASE_QUALITY_TO_USE = (byte) 8;
protected PrintStream graphWriter = null;
protected byte minBaseQualityToUseInAssembly = DEFAULT_MIN_BASE_QUALITY_TO_USE;

6
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
View File

@ -64,7 +64,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleComplex1() {
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "c0379d32c8c743d84c6da5956d67c004");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "57e13aed8dc483514ac15fb757aee1d1");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -88,12 +88,12 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleGGAComplex() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
"2fb56d241baca3658af5811e680bde4c");
"d89c8a32e9c54f66e0331382cac86b27");
}
@Test
public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
"bd7d24e87776f939b36742c1fd33b25c");
"89a28d4290523dd55117bc4e44212d73");
}
}

16
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -80,12 +80,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "943302eb9b9798d1ffeb9136612cbc85");
HCTest(CEUTRIO_BAM, "", "aeab5f0d40852e6332b96481981a0e46");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "3199bebe4e34b5df7558f74b05fb3a4e");
HCTest(NA12878_BAM, "", "c1530f2158cb41d50e830ca5be0f97a0");
}
@Test(enabled = false) // can't annotate the rsID's yet
@ -96,7 +96,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
"aef51f79d58634e4b35a1a98caba329c");
"3e2e4a62c6c60d432fa1ca32aee2635b");
}
@Test
@ -112,7 +112,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "5ac0d4b30a0c9a97a71ad014e63f11cf");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "bac6f98e910290722df28da44b41f06f");
}
private void HCTestNearbySmallIntervals(String bam, String args, String md5) {
@ -149,7 +149,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerNearbySmallIntervals() {
HCTestNearbySmallIntervals(NA12878_BAM, "", "a7e3b05fdc9866965e3ab71dbbd288ff");
HCTestNearbySmallIntervals(NA12878_BAM, "", "65e7b1b72a2411d6360138049914aa3a");
}
// This problem bam came from a user on the forum and it spotted a problem where the ReadClipper
@ -166,7 +166,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void HCTestStructuralIndels() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("8252f956e94cb8538b18210e9350f0e3"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("ab518ae32535714604a4ffc71fe42511"));
executeTest("HCTestStructuralIndels: ", spec);
}
@ -188,7 +188,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestReducedBam() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
Arrays.asList("7d4da215e86658e8da70fa0ade7f3eca"));
Arrays.asList("3c87eb93ffe3a0166aca753050b981e1"));
executeTest("HC calling on a ReducedRead BAM", spec);
}
@ -196,7 +196,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void testReducedBamWithReadsNotFullySpanningDeletion() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "reduced.readNotFullySpanningDeletion.bam -o %s -L 1:167871297", 1,
Arrays.asList("b0f0467dd4bfc4cdc85fff85ffa6f0c1"));
Arrays.asList("8adfa8a27a312760dab50787da595c57"));
executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec);
}
}