zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

I figured out why we were getting tons of hom var genotype calls with Mauricio's low quality (synthetic) reduced reads: the RR implementation in the UG was not capping the base quality by the mapping quality, so all the low quality reads were used to generate GLs. Fixed.

This commit is contained in:
Eric Banks 2011-11-18 12:29:15 -05:00
parent bad19779b9
commit 768b27322b
1 changed files with 18 additions and 19 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

37
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
View File

@ -28,7 +28,6 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import net.sf.samtools.SAMUtils; import net.sf.samtools.SAMUtils;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.fragments.FragmentCollection; import org.broadinstitute.sting.utils.fragments.FragmentCollection;
import org.broadinstitute.sting.utils.fragments.FragmentUtils;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
@ -275,19 +274,20 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
public int add(PileupElement elt, boolean ignoreBadBases, boolean capBaseQualsAtMappingQual, int minBaseQual) { public int add(PileupElement elt, boolean ignoreBadBases, boolean capBaseQualsAtMappingQual, int minBaseQual) {
byte obsBase = elt.getBase(); byte obsBase = elt.getBase();
byte qual = qualToUse(elt, ignoreBadBases, capBaseQualsAtMappingQual, minBaseQual);
if ( elt.isReducedRead() ) { if ( elt.isReducedRead() ) {
// reduced read representation // reduced read representation
byte qual = elt.getQual(); if ( BaseUtils.isRegularBase( obsBase )) {
if ( BaseUtils.isRegularBase( elt.getBase() )) {
add(obsBase, qual, (byte)0, (byte)0, elt.getRepresentativeCount()); // fast calculation of n identical likelihoods add(obsBase, qual, (byte)0, (byte)0, elt.getRepresentativeCount()); // fast calculation of n identical likelihoods
return elt.getRepresentativeCount(); // we added nObs bases here return elt.getRepresentativeCount(); // we added nObs bases here
} else // odd bases or deletions => don't use them }
return 0;
} else { // odd bases or deletions => don't use them
byte qual = qualToUse(elt, ignoreBadBases, capBaseQualsAtMappingQual, minBaseQual); return 0;
return qual > 0 ? add(obsBase, qual, (byte)0, (byte)0, 1) : 0;
} }
return qual > 0 ? add(obsBase, qual, (byte)0, (byte)0, 1) : 0;
} }
public int add(List<PileupElement> overlappingPair, boolean ignoreBadBases, boolean capBaseQualsAtMappingQual, int minBaseQual) { public int add(List<PileupElement> overlappingPair, boolean ignoreBadBases, boolean capBaseQualsAtMappingQual, int minBaseQual) {
@ -511,20 +511,19 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
* @return * @return
*/ */
private static byte qualToUse(PileupElement p, boolean ignoreBadBases, boolean capBaseQualsAtMappingQual, int minBaseQual) { private static byte qualToUse(PileupElement p, boolean ignoreBadBases, boolean capBaseQualsAtMappingQual, int minBaseQual) {
if ( ignoreBadBases && !BaseUtils.isRegularBase( p.getBase() ) ) { if ( ignoreBadBases && !BaseUtils.isRegularBase( p.getBase() ) )
return 0; return 0;
} else {
byte qual = p.getQual();
if ( qual > SAMUtils.MAX_PHRED_SCORE ) byte qual = p.getQual();
throw new UserException.MalformedBAM(p.getRead(), String.format("the maximum allowed quality score is %d, but a quality of %d was observed in read %s. Perhaps your BAM incorrectly encodes the quality scores in Sanger format; see http://en.wikipedia.org/wiki/FASTQ_format for more details", SAMUtils.MAX_PHRED_SCORE, qual, p.getRead().getReadName()));
if ( capBaseQualsAtMappingQual )
qual = (byte)Math.min((int)p.getQual(), p.getMappingQual());
if ( (int)qual < minBaseQual )
qual = (byte)0;
return qual; if ( qual > SAMUtils.MAX_PHRED_SCORE )
} throw new UserException.MalformedBAM(p.getRead(), String.format("the maximum allowed quality score is %d, but a quality of %d was observed in read %s. Perhaps your BAM incorrectly encodes the quality scores in Sanger format; see http://en.wikipedia.org/wiki/FASTQ_format for more details", SAMUtils.MAX_PHRED_SCORE, qual, p.getRead().getReadName()));
if ( capBaseQualsAtMappingQual )
qual = (byte)Math.min((int)p.getQual(), p.getMappingQual());
if ( (int)qual < minBaseQual )
qual = (byte)0;
return qual;
} }
// ----------------------------------------------------------------------------------------------------------------- // -----------------------------------------------------------------------------------------------------------------