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Merge pull request #1017 from broadinstitute/ldg_contaminationDS 

Enable contamination correction via downsampling (as for HaplotypeCal…
This commit is contained in:
kcibul 2015-06-15 14:37:10 -04:00
parent 9522be8762 ce5ecf1383
commit 578d429348
3 changed files with 13 additions and 3 deletions
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2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
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@ -85,7 +85,7 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<AssemblyBa
private MergeVariantsAcrossHaplotypes crossHaplotypeEventMerger;
private final boolean doPhysicalPhasing;
protected final boolean doPhysicalPhasing;
private final GenotypingModel genotypingModel;

5
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java
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@ -102,6 +102,11 @@ public final class GATKVCFConstants {
public static final String TUMOR_LOD_KEY = "TLOD"; //M2
public static final String VARIANT_TYPE_KEY = "VariantType";
public static final String VQS_LOD_KEY = "VQSLOD";
public static final String OXOG_ALT_F1R2_KEY = "ALT_F1R2";
public static final String OXOG_ALT_F2R1_KEY = "ALT_F2R1";
public static final String OXOG_REF_F1R2_KEY = "REF_F1R2";
public static final String OXOG_REF_F2R1_KEY = "REF_F2R1";
public static final String OXOG_FRACTION_KEY = "FOXOG";
//FORMAT keys
public static final String ALLELE_BALANCE_KEY = "AB";

9
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java
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@ -63,13 +63,13 @@ public class GATKVCFHeaderLines {
// M2-related filters
addFilterLine(new VCFFilterHeaderLine(GATKVCFConstants.ALT_ALLELE_IN_NORMAL_FILTER_NAME, "Evidence seen in the normal sample"));
addFilterLine(new VCFFilterHeaderLine(GATKVCFConstants.CLUSTERED_EVENTS_FILTER_NAME, "Clustered events observed in the tumor "));
addFilterLine(new VCFFilterHeaderLine(GATKVCFConstants.CLUSTERED_EVENTS_FILTER_NAME, "Clustered events observed in the tumor"));
addFilterLine(new VCFFilterHeaderLine(GATKVCFConstants.GERMLINE_RISK_FILTER_NAME, "Evidence indicates this site is germline, not somatic"));
addFilterLine(new VCFFilterHeaderLine(GATKVCFConstants.HOMOLOGOUS_MAPPING_EVENT_FILTER_NAME, "More than three events were observed in the tumor"));
addFilterLine(new VCFFilterHeaderLine(GATKVCFConstants.MULTI_EVENT_ALT_ALLELE_IN_NORMAL_FILTER_NAME, "Multiple events observed in tumor and normal"));
addFilterLine(new VCFFilterHeaderLine(GATKVCFConstants.PON_FILTER_NAME, "Seen in at least 2 samples in the panel of normals"));
addFilterLine(new VCFFilterHeaderLine(GATKVCFConstants.TUMOR_LOD_FILTER_NAME, "Tumor does not meet likelihood threshold"));
addFilterLine(new VCFFilterHeaderLine(GATKVCFConstants.STR_CONTRACTION_FILTER_NAME, "Site filtered due to contraction of short repeat region"));
addFilterLine(new VCFFilterHeaderLine(GATKVCFConstants.STR_CONTRACTION_FILTER_NAME, "Site filtered due to contraction of short tandem repeat region"));
addFormatLine(new VCFFormatHeaderLine(ALLELE_BALANCE_KEY, 1, VCFHeaderLineType.Float, "Allele balance for each het genotype"));
addFormatLine(new VCFFormatHeaderLine(MAPPING_QUALITY_ZERO_BY_SAMPLE_KEY, 1, VCFHeaderLineType.Integer, "Number of Mapping Quality Zero Reads per sample"));
@ -96,6 +96,11 @@ public class GATKVCFHeaderLines {
// M2-related info lines
addFormatLine(new VCFFormatHeaderLine(GATKVCFConstants.ALLELE_FRACTION_KEY, 1, VCFHeaderLineType.Float, "Allele fraction of the event in the tumor"));
addFormatLine(new VCFFormatHeaderLine(GATKVCFConstants.OXOG_ALT_F1R2_KEY, 1, VCFHeaderLineType.Integer, "Count of reads in F1R2 pair orientation supporting the alternate allele"));
addFormatLine(new VCFFormatHeaderLine(GATKVCFConstants.OXOG_ALT_F2R1_KEY, 1, VCFHeaderLineType.Integer, "Count of reads in F2R1 pair orientation supporting the alternate allele"));
addFormatLine(new VCFFormatHeaderLine(GATKVCFConstants.OXOG_REF_F1R2_KEY, 1, VCFHeaderLineType.Integer, "Count of reads in F1R2 pair orientation supporting the reference allele"));
addFormatLine(new VCFFormatHeaderLine(GATKVCFConstants.OXOG_REF_F2R1_KEY, 1, VCFHeaderLineType.Integer, "Count of reads in F2R1 pair orientation supporting the reference allele"));
addFormatLine(new VCFFormatHeaderLine(GATKVCFConstants.OXOG_FRACTION_KEY, 1, VCFHeaderLineType.Float, "Fraction of alt reads indicating OxoG error"));
addInfoLine(new VCFInfoHeaderLine(MLE_ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"));