diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java index f8714d0ca..c5bc119f0 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java @@ -144,6 +144,7 @@ public final class GATKVCFConstants { public static final String PON_FILTER_NAME = "panel_of_normals"; //M2 public static final String STR_CONTRACTION_FILTER_NAME = "str_contraction"; //M2 public static final String TUMOR_LOD_FILTER_NAME = "t_lod_fstar"; //M2 + public static final String TRIALLELIC_SITE_FILTER_NAME = "triallelic_site"; //M2 // Symbolic alleles public final static String SYMBOLIC_ALLELE_DEFINITION_HEADER_TAG = "ALT"; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java index f5aa6bddf..e18e1b4ea 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java @@ -70,6 +70,7 @@ public class GATKVCFHeaderLines { 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 tandem repeat region")); + addFilterLine(new VCFFilterHeaderLine(GATKVCFConstants.TRIALLELIC_SITE_FILTER_NAME, "Site filtered because more than two alt alleles pass tumor LOD")); 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"));