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

Merge pull request #336 from broadinstitute/gda_ancient_dna_pls 

Last feature request from Reich/Paavo labs: the allSitePLs feature in UG...
This commit is contained in:
Eric Banks 2013-07-18 10:47:52 -07:00
parent 234f564009 9dd109b79a
commit bf5ce41321
4 changed files with 10 additions and 8 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

9
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
View File

@ -147,13 +147,6 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
// if we only want variants, then we don't need to calculate genotype likelihoods
if ( UAC.OutputMode == UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_VARIANTS_ONLY )
return builder.make();
// if user requires all PLs at all sites, add all possible alt alleles
else if (UAC.annotateAllSitesWithPLs) {
for ( final byte base : BaseUtils.BASES ) {
if ( base != refBase )
alleles.add(Allele.create(base));
}
}
else
// otherwise, choose any alternate allele (it doesn't really matter)
@ -199,6 +192,8 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
final double[] genotypeLikelihoods = MathUtils.normalizeFromLog10(myLikelihoods, false, true);
gb.PL(genotypeLikelihoods);
gb.DP(sampleData.depth);
if (UAC.annotateAllSitesWithPLs)
gb.attribute(UnifiedGenotyperEngine.PL_FOR_ALL_SNP_ALLELES_KEY,GenotypeLikelihoods.fromLog10Likelihoods(MathUtils.normalizeFromLog10(allLikelihoods, false, true)));
genotypes.add(gb.make());
}

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -318,6 +318,9 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
headerInfo.add(new VCFInfoHeaderLine(VCFConstants.REFSAMPLE_DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Total reference sample depth"));
}
if (UAC.annotateAllSitesWithPLs) {
headerInfo.add(new VCFFormatHeaderLine(UnifiedGenotyperEngine.PL_FOR_ALL_SNP_ALLELES_KEY, 10, VCFHeaderLineType.Integer, "Phred-scaled genotype likelihoods for all 4 possible bases regardless of whether there is statistical evidence for them. Ordering is always PL for AA AC CC GA GC GG TA TC TG TT."));
}
VCFStandardHeaderLines.addStandardInfoLines(headerInfo, true,
VCFConstants.DOWNSAMPLED_KEY,
VCFConstants.MLE_ALLELE_COUNT_KEY,

1
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -79,6 +79,7 @@ public class UnifiedGenotyperEngine {
private static final String GPSTRING = "GENERALPLOIDY";
public static final String NUMBER_OF_DISCOVERED_ALLELES_KEY = "NDA";
public static final String PL_FOR_ALL_SNP_ALLELES_KEY = "APL";
public static final double HUMAN_SNP_HETEROZYGOSITY = 1e-3;
public static final double HUMAN_INDEL_HETEROZYGOSITY = 1e-4;

5
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -164,7 +164,10 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void emitPLsAtAllSites() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --output_mode EMIT_ALL_SITES -allSitePLs", 1,
Arrays.asList("7cc55db8693759e059a05bc4398f6f69"));
Arrays.asList("552aced1b1ef7e4a554223f4719f9560"));
// GDA: TODO: BCF encoder/decoder doesn't seem to support non-standard values in genotype fields. IE even if there is a field defined in FORMAT and in the header the BCF2 encoder will still fail
spec1.disableShadowBCF();
executeTest("test all site PLs 1", spec1);
}