Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fix GT header in PostprocessGermlineCNVCalls's --output-genotyped-intervals output #8621

Merged
merged 2 commits into from
Dec 14, 2023
Merged

Fix GT header in PostprocessGermlineCNVCalls's --output-genotyped-intervals output #8621

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
7b64554
Write gCNV interval output ID=GT header as Type=String
jmarshall Dec 13, 2023
42b67ad
Use correct header types and numbers in test VCF file
jmarshall Dec 13, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion ...g/broadinstitute/hellbender/tools/copynumber/gcnv/GermlineCNVIntervalVariantComposer.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
14 changes: 7 additions & 7 deletions ...st/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFUnitTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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;
}
Expand Down
Loading