Source:
<code>public void onTraversalStart() { final VCFHeader inputHeader = getHeaderForVariants(); final Set<VCFHeaderLine> headerLines = new HashSet<>(inputHeader.getMetaDataInSortedOrder()); Mutect2FilteringEngine.M_2_FILTER_NAMES.stream().map(GATKVCFHeaderLines::getFilterLine).forEach(headerLines::add); headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.ARTIFACT_IN_NORMAL_FILTER_NAME, "artifact_in_normal")); headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.MEDIAN_BASE_QUALITY_DIFFERENCE_FILTER_NAME, "ref - alt median base quality")); headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.MEDIAN_MAPPING_QUALITY_DIFFERENCE_FILTER_NAME, "ref - alt median mapping quality")); headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.MEDIAN_CLIPPING_DIFFERENCE_FILTER_NAME, "ref - alt median clipping")); headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.MEDIAN_FRAGMENT_LENGTH_DIFFERENCE_FILTER_NAME, "abs(ref - alt) median fragment length")); headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.READ_POSITION_FILTER_NAME, "median distance of alt variants from end of reads")); headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.CONTAMINATION_FILTER_NAME, "contamination")); <START> headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.DUPLICATED_EVIDENCE_FILTER_NAME, "alt reads are mostly duplicate reads")); <END> final VCFHeader vcfHeader = new VCFHeader(headerLines, inputHeader.getGenotypeSamples()); vcfWriter = createVCFWriter(new File(outputVcf)); vcfWriter.writeHeader(vcfHeader); }</code><technical_language>I suggest instead of "alt reads duplicate reads" use, "evidence for alt allele is overrepresented apparent duplicates"</technical_language>

Target:
public void onTraversalStart() { final VCFHeader inputHeader = getHeaderForVariants(); final Set<VCFHeaderLine> headerLines = new HashSet<>(inputHeader.getMetaDataInSortedOrder()); Mutect2FilteringEngine.M_2_FILTER_NAMES.stream().map(GATKVCFHeaderLines::getFilterLine).forEach(headerLines::add); headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.ARTIFACT_IN_NORMAL_FILTER_NAME, "artifact_in_normal")); headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.MEDIAN_BASE_QUALITY_DIFFERENCE_FILTER_NAME, "ref - alt median base quality")); headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.MEDIAN_MAPPING_QUALITY_DIFFERENCE_FILTER_NAME, "ref - alt median mapping quality")); headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.MEDIAN_CLIPPING_DIFFERENCE_FILTER_NAME, "ref - alt median clipping")); headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.MEDIAN_FRAGMENT_LENGTH_DIFFERENCE_FILTER_NAME, "abs(ref - alt) median fragment length")); headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.READ_POSITION_FILTER_NAME, "median distance of alt variants from end of reads")); headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.CONTAMINATION_FILTER_NAME, "contamination")); headerLines.addAll(getDefaultToolVCFHeaderLines()); headerLines.add(new VCFFilterHeaderLine(Mutect2FilteringEngine.DUPLICATED_EVIDENCE_FILTER_NAME, "evidence for alt allele is overrepresented by apparent duplicates")); final VCFHeader vcfHeader = new VCFHeader(headerLines, inputHeader.getGenotypeSamples()); vcfWriter = createVCFWriter(new File(outputVcf)); vcfWriter.writeHeader(vcfHeader); }