public static void addVQSRStandardHeaderLines(final Set<VCFHeaderLine> hInfo) {
hInfo.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.END_KEY));
hInfo.add(
new VCFInfoHeaderLine(
VariantRecalibrator.VQS_LOD_KEY,
1,
VCFHeaderLineType.Float,
"Log odds ratio of being a true variant versus being false under the trained gaussian mixture model"));
hInfo.add(
new VCFInfoHeaderLine(
VariantRecalibrator.CULPRIT_KEY,
1,
VCFHeaderLineType.String,
"The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out"));
hInfo.add(
new VCFInfoHeaderLine(
VariantRecalibrator.POSITIVE_LABEL_KEY,
1,
VCFHeaderLineType.Flag,
"This variant was used to build the positive training set of good variants"));
hInfo.add(
new VCFInfoHeaderLine(
VariantRecalibrator.NEGATIVE_LABEL_KEY,
1,
VCFHeaderLineType.Flag,
"This variant was used to build the negative training set of bad variants"));
}
/**
* Gets the header lines for the VCF writer
*
* @return A set of VCF header lines
*/
private static Set<VCFHeaderLine> getHeaderInfo() {
Set<VCFHeaderLine> headerLines = new HashSet<>();
// INFO fields for overall data
headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.END_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AVG_INTERVAL_DP_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.INTERVAL_GC_CONTENT_KEY));
headerLines.add(
new VCFInfoHeaderLine(
"Diagnose Targets", 0, VCFHeaderLineType.Flag, "DiagnoseTargets mode"));
// FORMAT fields for each genotype
headerLines.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_FILTER_KEY));
headerLines.add(
GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.AVG_INTERVAL_DP_BY_SAMPLE_KEY));
headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.LOW_COVERAGE_LOCI));
headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.ZERO_COVERAGE_LOCI));
// FILTER fields
for (CallableStatus stat : CallableStatus.values())
headerLines.add(new VCFFilterHeaderLine(stat.name(), stat.description));
return headerLines;
}
private void writeRecord(VariantContext vc, RefMetaDataTracker tracker, GenomeLoc loc) {
if (!wroteHeader) {
wroteHeader = true;
// setup the header fields
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variants.getName())));
hInfo.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_KEY));
allowedGenotypeFormatStrings.add(VCFConstants.GENOTYPE_KEY);
for (VCFHeaderLine field : hInfo) {
if (field instanceof VCFFormatHeaderLine) {
allowedGenotypeFormatStrings.add(((VCFFormatHeaderLine) field).getID());
}
}
samples = new LinkedHashSet<String>();
if (sampleName != null) {
samples.add(sampleName);
} else {
// try VCF first
samples =
SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName()));
if (samples.isEmpty()) {
List<Feature> features = tracker.getValues(variants, loc);
if (features.size() == 0)
throw new IllegalStateException(
"No rod data is present, but we just created a VariantContext");
Feature f = features.get(0);
if (f instanceof RawHapMapFeature)
samples.addAll(Arrays.asList(((RawHapMapFeature) f).getSampleIDs()));
else samples.addAll(vc.getSampleNames());
}
}
vcfwriter.writeHeader(new VCFHeader(hInfo, samples));
}
vc = GATKVariantContextUtils.purgeUnallowedGenotypeAttributes(vc, allowedGenotypeFormatStrings);
vcfwriter.add(vc);
}