From 7b64554ec6fb811d7c24f9238741c3318fc3fcb0 Mon Sep 17 00:00:00 2001 From: John Marshall Date: Wed, 13 Dec 2023 17:02:20 +1300 Subject: [PATCH 1/2] Write gCNV interval output ID=GT header as Type=String Incorrectly writing this as Type=Integer causes bcftools to misparse the genotype field. --- .../copynumber/gcnv/GermlineCNVIntervalVariantComposer.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/gcnv/GermlineCNVIntervalVariantComposer.java b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/gcnv/GermlineCNVIntervalVariantComposer.java index 421dda1ec1d..3c34b34bf43 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/gcnv/GermlineCNVIntervalVariantComposer.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/gcnv/GermlineCNVIntervalVariantComposer.java @@ -95,7 +95,7 @@ public void composeVariantContextHeader(final SAMSequenceDictionary sequenceDict /* header lines related to genotype formatting */ result.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, - VCFHeaderLineType.Integer, "Genotype")); + VCFHeaderLineType.String, "Genotype")); result.addMetaDataLine(new VCFFormatHeaderLine(CN, 1, VCFHeaderLineType.Integer, "Copy number maximum a posteriori value")); result.addMetaDataLine(new VCFFormatHeaderLine(CNLP, VCFHeaderLineCount.UNBOUNDED, From 42b67ad149829de097393c3b85b852dd8b6c2eb1 Mon Sep 17 00:00:00 2001 From: John Marshall Date: Wed, 13 Dec 2023 17:04:06 +1300 Subject: [PATCH 2/2] Use correct header types and numbers in test VCF file --- .../walkers/variantutils/ReblockGVCFUnitTest.java | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFUnitTest.java index 9ee3d08682b..3a15b204383 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFUnitTest.java @@ -408,16 +408,16 @@ private GVCFWriter setUpWriter(final File outputFile, final File dictionary) thr result.setSequenceDictionary(dict); result.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "genotype")); - result.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_ALLELE_DEPTHS, 1, - VCFHeaderLineType.String, "Allele depth")); + result.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_ALLELE_DEPTHS, VCFHeaderLineCount.R, + VCFHeaderLineType.Integer, "Allele depth")); result.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, - VCFHeaderLineType.String, " depth")); + VCFHeaderLineType.Integer, " depth")); result.addMetaDataLine(new VCFInfoHeaderLine(VCFConstants.DEPTH_KEY, 1, - VCFHeaderLineType.String, " depth")); + VCFHeaderLineType.Integer, " depth")); result.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_QUALITY_KEY, 1, - VCFHeaderLineType.String, "Genotype quality")); - result.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_PL_KEY, 1, - VCFHeaderLineType.String, "Phred-scaled likelihoods")); + VCFHeaderLineType.Integer, "Genotype quality")); + result.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_PL_KEY, VCFHeaderLineCount.G, + VCFHeaderLineType.Integer, "Phred-scaled likelihoods")); gvcfWriter.writeHeader(result); return gvcfWriter; }