correct some Mutect2 VCF header lines (#5792)

broadinstitute · Mar 13, 2019 · d8d06cd · d8d06cd
1 parent a6c89de
commit d8d06cd
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java
@@ -216,9 +216,9 @@ public static VCFFormatHeaderLine getEquivalentFormatHeaderLine(final String inf
         addFormatLine(new VCFFormatHeaderLine(TUMOR_LOD_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Log odds ratio score for variant"));
         addInfoLine(new VCFInfoHeaderLine(IN_PON_VCF_ATTRIBUTE, 0, VCFHeaderLineType.Flag, "site found in panel of normals"));
         addInfoLine(new VCFInfoHeaderLine(POPULATION_AF_VCF_ATTRIBUTE, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "negative-log-10 population allele frequencies of alt alleles"));
-        addInfoLine(new VCFInfoHeaderLine(GERMLINE_QUAL_VCF_ATTRIBUTE, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Phred-scaled qualities that alt allele are not germline variants"));
-        addInfoLine(new VCFInfoHeaderLine(SEQUENCING_QUAL_VCF_ATTRIBUTE, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Phred-scaled qualities that alt allele are not sequencing errors"));
-        addInfoLine(new VCFInfoHeaderLine(POLYMERASE_SLIPPAGE_QUAL_VCF_ATTRIBUTE, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Phred-scaled qualities that alt alleles in STRs are not polymerase slippage errors"));
+        addInfoLine(new VCFInfoHeaderLine(GERMLINE_QUAL_VCF_ATTRIBUTE, 1, VCFHeaderLineType.Integer, "Phred-scaled quality that alt alleles are not germline variants"));
+        addInfoLine(new VCFInfoHeaderLine(SEQUENCING_QUAL_VCF_ATTRIBUTE, 1, VCFHeaderLineType.Integer, "Phred-scaled quality that alt alleles are not sequencing errors"));
+        addInfoLine(new VCFInfoHeaderLine(POLYMERASE_SLIPPAGE_QUAL_VCF_ATTRIBUTE, 1, VCFHeaderLineType.Integer, "Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors"));
         addInfoLine(new VCFInfoHeaderLine(STRAND_QUAL_VCF_ATTRIBUTE, 1, VCFHeaderLineType.Integer, "Phred-scaled quality of strand bias artifact"));
         addInfoLine(new VCFInfoHeaderLine(CONTAMINATION_QUAL_ATTRIBUTE, 1, VCFHeaderLineType.Float, "Phred-scaled qualities that alt allele are not due to contamination"));
         addInfoLine(new VCFInfoHeaderLine(NORMAL_ARTIFACT_LOD_ATTRIBUTE, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Negative log odds of artifact in normal with same allele fraction as tumor"));