From d8d06cd769959b595132cb0aab18ccd7fe913ffd Mon Sep 17 00:00:00 2001 From: David Benjamin Date: Wed, 13 Mar 2019 11:04:15 -0400 Subject: [PATCH] correct some Mutect2 VCF header lines (#5792) --- .../hellbender/utils/variant/GATKVCFHeaderLines.java | 6 +++--- 1 file changed, 3 insertions(+), 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 index 6bdefa4b01a..3ee62b914c7 100644 --- 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"));