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As per quick chat with Richard Durban, don't increase the mapping quality of realigned reads too much; for now, arbitrarily increase the MQ by 10. We need to figure out a better solution. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3731 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-07-07 20:12:59 +00:00
parent 8ff1a4b929
commit 30714ec8d9
2 changed files with 8 additions and 10 deletions
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12
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
View File

@ -550,17 +550,15 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
} catch (Exception e) {}
}
// We need to update the mapping quality score of the cleaned reads;
// however we don't have enough info to use the proper MAQ scoring system.
// For now, we'll use a heuristic:
// the mapping quality score is improved by the LOD difference in mismatching
// bases between the reference and alternate consensus (divided by 10)
// finish cleaning the appropriate reads
for ( Pair<Integer, Integer> indexPair : bestConsensus.readIndexes ) {
final AlignedRead aRead = altReads.get(indexPair.first);
if ( aRead.finalizeUpdate() ) {
aRead.getRead().setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + (int)(improvement/10.0), 255));
// We need to update the mapping quality score of the cleaned reads;
// however we don't have enough info to use the proper MAQ scoring system.
// For now, we will just arbitrarily add 10 to the mapping quality. [EB, 6/7/2010].
// TODO -- we need a better solution here
aRead.getRead().setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + 10, 254));
aRead.getRead().setAttribute("NM", AlignmentUtils.numMismatches(aRead.getRead(), reference, aRead.getRead().getAlignmentStart()-(int)leftmostIndex));
}
}

6
java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
View File

@ -9,7 +9,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
@Test
public void testRealignerLod5() {
String[] md5s = {"56f1fb75cae706a5a6278257ea2f2598", "18fca887d1eb7dc300e717ae03b9da62"};
String[] md5s = {"726c629a382e4da0dffd4de2e439aa91", "18fca887d1eb7dc300e717ae03b9da62"};
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -LOD 5 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
2,
@ -19,7 +19,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
@Test
public void testRealignerLod50() {
String[] md5s = {"56f1fb75cae706a5a6278257ea2f2598", "9537e4f195ce5840136f60fb61201369"};
String[] md5s = {"726c629a382e4da0dffd4de2e439aa91", "9537e4f195ce5840136f60fb61201369"};
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -LOD 50 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
2,
@ -29,7 +29,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
@Test
public void testRealignerKnownsOnly() {
String[] md5s = {"54621fe4a53a559908ff20f6f0d0e758", "1091436c40d5ba557d85662999cc0c1d"};
String[] md5s = {"d609430ffbc0fd8b68f383b9eec17e8b", "1091436c40d5ba557d85662999cc0c1d"};
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -LOD 1.0 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10076000 -compress 1 -targetIntervals " + validationDataLocation + "NA12878.indels.intervals -B knownIndels,VCF," + validationDataLocation + "NA12878.indels.vcf -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -knownsOnly",
2,