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In order to be considered an informative read in the PerReadAlleleLikelihoodMap it has to be informative compared to all other alleles not just the worst allele. Also, fixing a bug when there is only one allele in the map.

This commit is contained in:
Ryan Poplin 2012-10-18 14:31:15 -04:00
parent 3504f71b6b
commit b4e69239dd
4 changed files with 17 additions and 21 deletions
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4
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java
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@ -70,12 +70,12 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","7d6f319b9edcb1ff8c290fef150a2df8");
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","9acfe0019efdc91217ee070acb071228");
}
@Test(enabled = true)
public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","dd02890123e07e7412a49475cb6280f1");
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","c1d4dd793f61710a1b1fc5d82803210f");
}
@Test(enabled = true)

4
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -21,7 +21,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "8c52c0955099cca3215a0d78fd455894");
HCTest(CEUTRIO_BAM, "", "75013fa6a884104f0b1797502b636698");
}
@Test
@ -31,7 +31,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles_for_indels 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "61c1a0fb62d909229af6b5a91dad8b35");
HCTest(CEUTRIO_BAM, "--max_alternate_alleles_for_indels 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "3cd3363976b1937d801f9f82996f4abe");
}
private void HCTestComplexVariants(String bam, String args, String md5) {

19
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PerReadAlleleLikelihoodMap.java
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@ -113,23 +113,20 @@ public class PerReadAlleleLikelihoodMap {
return likelihoodReadMap.get(p.getRead());
}
public static Allele getMostLikelyAllele(Map<Allele,Double> alleleMap) {
double minLike = Double.POSITIVE_INFINITY, maxLike = Double.NEGATIVE_INFINITY;
public static Allele getMostLikelyAllele( final Map<Allele,Double> alleleMap ) {
double maxLike = Double.NEGATIVE_INFINITY;
double prevMaxLike = Double.NEGATIVE_INFINITY;
Allele mostLikelyAllele = Allele.NO_CALL;
for (Map.Entry<Allele,Double> el : alleleMap.entrySet()) {
for (final Map.Entry<Allele,Double> el : alleleMap.entrySet()) {
if (el.getValue() > maxLike) {
prevMaxLike = maxLike;
maxLike = el.getValue();
mostLikelyAllele = el.getKey();
} else if( el.getValue() > prevMaxLike ) {
prevMaxLike = el.getValue();
}
if (el.getValue() < minLike)
minLike = el.getValue();
}
if (maxLike-minLike > INDEL_LIKELIHOOD_THRESH)
return mostLikelyAllele;
else
return Allele.NO_CALL;
return (maxLike - prevMaxLike > INDEL_LIKELIHOOD_THRESH ? mostLikelyAllele : Allele.NO_CALL );
}
}

11
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -60,7 +60,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultipleSNPAlleles() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
Arrays.asList("26af30187316f742878c85f0ed091837"));
Arrays.asList("48b4f4b05461be276bffc91350f08cbc"));
executeTest("test Multiple SNP alleles", spec);
}
@ -76,7 +76,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testReverseTrim() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
Arrays.asList("aa9cf96ab8f5aa844387e3aef1f27249"));
Arrays.asList("04affcc9d720ee17bc221759707e0cd2"));
executeTest("test reverse trim", spec);
}
@ -84,7 +84,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMismatchedPLs() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
Arrays.asList("d210ee1baa75dd4a0c63aef6b1fa7a8a"));
Arrays.asList("112e7bedfd284d4d9390aa006118c733"));
executeTest("test mismatched PLs", spec);
}
@ -343,13 +343,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSampleIndels1() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
Arrays.asList("7fc488fe16dea9f023bfcfdaa908a548"));
Arrays.asList("863ee56b3594f09795644127f2f9539f"));
List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
"low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
Arrays.asList("f3ff7fe0f15f31eadd726c711d6bf3de"));
Arrays.asList("503ca1b75cc7b2679eaa80f7b5e7ef1c"));
executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
}
@ -452,5 +452,4 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
Arrays.asList("bbf16e1873e525ee5975021cfb8988cf"));
executeTest("test calling on a ReducedRead BAM", spec);
}
}