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Better precision for the calculated AF value. Now looks at the total number of samples to determine how much precision is necessary. Also, changing default min BQ used for calling in UGv2 to Q17. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4655 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-11-12 08:31:40 +00:00
parent ec83a4b765
commit 69de3e51bf
3 changed files with 19 additions and 14 deletions
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29
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
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@ -112,31 +112,36 @@ public class VariantContextUtils {
// if there are alternate alleles, record the relevant tags
if ( vc.getAlternateAlleles().size() > 0 ) {
ArrayList<Double> alleleFreqs = new ArrayList<Double>();
ArrayList<String> alleleFreqs = new ArrayList<String>();
ArrayList<Integer> alleleCounts = new ArrayList<Integer>();
double totalChromosomes = (double)vc.getChromosomeCount();
for ( Allele allele : vc.getAlternateAlleles() ) {
alleleCounts.add(vc.getChromosomeCount(allele));
alleleFreqs.add((double)vc.getChromosomeCount(allele) / (double)vc.getChromosomeCount());
int altChromosomes = vc.getChromosomeCount(allele);
alleleCounts.add(altChromosomes);
String freq = String.format(makePrecisionFormatStringFromDenominatorValue(totalChromosomes), ((double)altChromosomes / totalChromosomes));
alleleFreqs.add(freq);
}
attributes.put(VCFConstants.ALLELE_COUNT_KEY, alleleCounts);
attributes.put(VCFConstants.ALLELE_FREQUENCY_KEY, alleleFreqs);
}
// // otherwise, remove them if present and requested
// else if ( removeStaleValues ) {
// if ( attributes.containsKey(VCFConstants.ALLELE_COUNT_KEY) )
// attributes.remove(VCFConstants.ALLELE_COUNT_KEY);
// if ( attributes.containsKey(VCFConstants.ALLELE_FREQUENCY_KEY) )
// attributes.remove(VCFConstants.ALLELE_FREQUENCY_KEY);
// }
// otherwise, set them to 0
else {
attributes.put(VCFConstants.ALLELE_COUNT_KEY, 0);
attributes.put(VCFConstants.ALLELE_FREQUENCY_KEY, 0.0);
}
}
private static String makePrecisionFormatStringFromDenominatorValue(double maxValue) {
int precision = 1;
while ( maxValue > 1 ) {
precision++;
maxValue /= 10.0;
}
return "%." + precision + "f";
}
/**
* A simple but common wrapper for matching VariantContext objects using JEXL expressions
*/

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -79,7 +79,7 @@ public class UnifiedArgumentCollection {
// control the various parameters to be used
@Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false)
public int MIN_BASE_QUALTY_SCORE = 20;
public int MIN_BASE_QUALTY_SCORE = 17;
@Argument(fullName = "min_mapping_quality_score", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for calling", required = false)
public int MIN_MAPPING_QUALTY_SCORE = 20;

2
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -25,7 +25,7 @@ public class
public void testMultiSamplePilot1Joint() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
Arrays.asList("9870dd089d0f76c8dd3e74bc9f2ba0f0"));
Arrays.asList("1dde074afe990fd38941de18bd35e188"));
executeTest("testMultiSamplePilot1 - Joint Estimate", spec);
}