1 package org.broadinstitute.hellbender.utils.variant; 2 3 import htsjdk.variant.vcf.*; 4 import org.broadinstitute.hellbender.tools.walkers.annotator.*; 5 import org.broadinstitute.hellbender.utils.Utils; 6 7 import java.util.*; 8 9 import static org.broadinstitute.hellbender.utils.variant.GATKVCFConstants.*; 10 11 /** 12 * This class contains the {@link VCFHeaderLine} definitions for the annotation keys in {@link GATKVCFConstants}. 13 * VCF-standard header lines are in {@link VCFStandardHeaderLines}, in htsjdk 14 */ 15 public class GATKVCFHeaderLines { 16 getInfoLine(final String id)17 public static VCFInfoHeaderLine getInfoLine(final String id) { 18 if (!infoLines.containsKey(id)) { 19 throw new IllegalStateException("No VCF INFO header line found for key " + id); 20 } 21 return infoLines.get(id); 22 } getFormatLine(final String id)23 public static VCFFormatHeaderLine getFormatLine(final String id) { 24 if (!formatLines.containsKey(id)) { 25 throw new IllegalStateException("No VCF FORMAT header line found for key " + id); 26 } 27 return formatLines.get(id); 28 } getFilterLine(final String id)29 public static VCFFilterHeaderLine getFilterLine(final String id) { 30 if (!filterLines.containsKey(id)) { 31 throw new IllegalStateException("No VCF FILTER header line found for key " + id); 32 } 33 return filterLines.get(id); 34 } 35 getAllInfoLines()36 public static Set<VCFInfoHeaderLine> getAllInfoLines() { return Collections.unmodifiableSet(new HashSet<>(infoLines.values())); } getAllFormatLines()37 public static Set<VCFFormatHeaderLine> getAllFormatLines() { return Collections.unmodifiableSet(new HashSet<>(formatLines.values())); } getAllFilterLines()38 public static Set<VCFFilterHeaderLine> getAllFilterLines() { return Collections.unmodifiableSet(new HashSet<>(filterLines.values())); } 39 40 private static final Map<String, VCFInfoHeaderLine> infoLines = new LinkedHashMap<>(60); 41 private static final Map<String, VCFFormatHeaderLine> formatLines = new LinkedHashMap<>(25); 42 private static final Map<String, VCFFilterHeaderLine> filterLines = new LinkedHashMap<>(2); 43 addFormatLine(final VCFFormatHeaderLine line)44 private static void addFormatLine(final VCFFormatHeaderLine line) { 45 Utils.nonNull(line); 46 formatLines.put(line.getID(), line); 47 } 48 addInfoLine(final VCFInfoHeaderLine line)49 private static void addInfoLine(final VCFInfoHeaderLine line) { 50 Utils.nonNull(line); 51 infoLines.put(line.getID(), line); 52 } 53 addFilterLine(final VCFFilterHeaderLine line)54 private static void addFilterLine(final VCFFilterHeaderLine line) { 55 Utils.nonNull(line); 56 filterLines.put(line.getID(), line); 57 } 58 getEquivalentFormatHeaderLine(final String infoFieldKey)59 public static VCFFormatHeaderLine getEquivalentFormatHeaderLine(final String infoFieldKey) { 60 final VCFInfoHeaderLine infoLine = getInfoLine(infoFieldKey); 61 if (infoLine.isFixedCount()) { 62 return new VCFFormatHeaderLine(infoLine.getID(), infoLine.getCount(), infoLine.getType(), infoLine.getDescription()); 63 } else { 64 return new VCFFormatHeaderLine(infoLine.getID(), infoLine.getCountType(), infoLine.getType(), infoLine.getDescription()); 65 } 66 } 67 68 static { addInfoLine(new VCFInfoHeaderLine(SB_TABLE_KEY, 4, VCFHeaderLineType.Integer, R))69 addInfoLine(new VCFInfoHeaderLine(SB_TABLE_KEY, 4, VCFHeaderLineType.Integer, "Forward/reverse read counts for strand bias tests")); addFormatLine(new VCFFormatHeaderLine(GENOTYPE_QUALITY_BY_ALLELE_BALANCE, 1, VCFHeaderLineType.Integer, R))70 addFormatLine(new VCFFormatHeaderLine(GENOTYPE_QUALITY_BY_ALLELE_BALANCE, 1, VCFHeaderLineType.Integer, ":")); addFormatLine(new VCFFormatHeaderLine(GENOTYPE_QUALITY_BY_ALT_CONFIDENCE, 1, VCFHeaderLineType.Integer, R))71 addFormatLine(new VCFFormatHeaderLine(GENOTYPE_QUALITY_BY_ALT_CONFIDENCE, 1, VCFHeaderLineType.Integer, ":")); addInfoLine(new VCFInfoHeaderLine(GATKVCFConstants.AC_ADJUSTED_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, R))72 addInfoLine(new VCFInfoHeaderLine(GATKVCFConstants.AC_ADJUSTED_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Allele count for each ALT, adjusted to represent high quality genotypes only")); 73 addFilterLine(new VCFFilterHeaderLine(LOW_QUAL_FILTER_NAME, R))74 addFilterLine(new VCFFilterHeaderLine(LOW_QUAL_FILTER_NAME, "Low quality")); addFilterLine(new VCFFilterHeaderLine(VCFConstants.PASSES_FILTERS_v4, R))75 addFilterLine(new VCFFilterHeaderLine(VCFConstants.PASSES_FILTERS_v4, "Site contains at least one allele that passes filters")); 76 77 // M2-related filters addFilterLine(new VCFFilterHeaderLine(ALIGNMENT_ARTIFACT_FILTER_NAME, R))78 addFilterLine(new VCFFilterHeaderLine(ALIGNMENT_ARTIFACT_FILTER_NAME, "Alignment artifact")); addFilterLine(new VCFFilterHeaderLine(CLUSTERED_EVENTS_FILTER_NAME, R))79 addFilterLine(new VCFFilterHeaderLine(CLUSTERED_EVENTS_FILTER_NAME, "Clustered events observed in the tumor")); addFilterLine(new VCFFilterHeaderLine(GERMLINE_RISK_FILTER_NAME, R))80 addFilterLine(new VCFFilterHeaderLine(GERMLINE_RISK_FILTER_NAME, "Evidence indicates this site is germline, not somatic")); addFilterLine(new VCFFilterHeaderLine(PON_FILTER_NAME, R))81 addFilterLine(new VCFFilterHeaderLine(PON_FILTER_NAME, "Blacklisted site in panel of normals")); addFilterLine(new VCFFilterHeaderLine(TUMOR_EVIDENCE_FILTER_NAME, R))82 addFilterLine(new VCFFilterHeaderLine(TUMOR_EVIDENCE_FILTER_NAME, "Mutation does not meet likelihood threshold")); addFilterLine(new VCFFilterHeaderLine(POLYMERASE_SLIPPAGE, R))83 addFilterLine(new VCFFilterHeaderLine(POLYMERASE_SLIPPAGE, "Site filtered due to contraction of short tandem repeat region")); addFilterLine(new VCFFilterHeaderLine(MULTIALLELIC_FILTER_NAME, R))84 addFilterLine(new VCFFilterHeaderLine(MULTIALLELIC_FILTER_NAME, "Site filtered because too many alt alleles pass tumor LOD")); addFilterLine(new VCFFilterHeaderLine(STRAND_ARTIFACT_FILTER_NAME, R))85 addFilterLine(new VCFFilterHeaderLine(STRAND_ARTIFACT_FILTER_NAME, "Evidence for alt allele comes from one read direction only")); addFilterLine(new VCFFilterHeaderLine(ARTIFACT_IN_NORMAL_FILTER_NAME, R))86 addFilterLine(new VCFFilterHeaderLine(ARTIFACT_IN_NORMAL_FILTER_NAME, "artifact_in_normal")); addFilterLine(new VCFFilterHeaderLine(MEDIAN_BASE_QUALITY_FILTER_NAME, R))87 addFilterLine(new VCFFilterHeaderLine(MEDIAN_BASE_QUALITY_FILTER_NAME, "alt median base quality")); addFilterLine(new VCFFilterHeaderLine(MEDIAN_MAPPING_QUALITY_FILTER_NAME, R))88 addFilterLine(new VCFFilterHeaderLine(MEDIAN_MAPPING_QUALITY_FILTER_NAME, "ref - alt median mapping quality")); addFilterLine(new VCFFilterHeaderLine(MEDIAN_FRAGMENT_LENGTH_DIFFERENCE_FILTER_NAME, R))89 addFilterLine(new VCFFilterHeaderLine(MEDIAN_FRAGMENT_LENGTH_DIFFERENCE_FILTER_NAME, "abs(ref - alt) median fragment length")); addFilterLine(new VCFFilterHeaderLine(READ_POSITION_FILTER_NAME, R))90 addFilterLine(new VCFFilterHeaderLine(READ_POSITION_FILTER_NAME, "median distance of alt variants from end of reads")); addFilterLine(new VCFFilterHeaderLine(CONTAMINATION_FILTER_NAME, R))91 addFilterLine(new VCFFilterHeaderLine(CONTAMINATION_FILTER_NAME, "contamination")); addFilterLine(new VCFFilterHeaderLine(DUPLICATED_EVIDENCE_FILTER_NAME, R))92 addFilterLine(new VCFFilterHeaderLine(DUPLICATED_EVIDENCE_FILTER_NAME, "evidence for alt allele is overrepresented by apparent duplicates")); addFilterLine(new VCFFilterHeaderLine(READ_ORIENTATION_ARTIFACT_FILTER_NAME, R))93 addFilterLine(new VCFFilterHeaderLine(READ_ORIENTATION_ARTIFACT_FILTER_NAME, "orientation bias detected by the orientation bias mixture model")); addFilterLine(new VCFFilterHeaderLine(BAD_HAPLOTYPE_FILTER_NAME, R))94 addFilterLine(new VCFFilterHeaderLine(BAD_HAPLOTYPE_FILTER_NAME, "Variant near filtered variant on same haplotype.")); addFilterLine(new VCFFilterHeaderLine(STRICT_STRAND_BIAS_FILTER_NAME, R))95 addFilterLine(new VCFFilterHeaderLine(STRICT_STRAND_BIAS_FILTER_NAME, "Evidence for alt allele is not represented in both directions")); addFilterLine(new VCFFilterHeaderLine(N_RATIO_FILTER_NAME, R))96 addFilterLine(new VCFFilterHeaderLine(N_RATIO_FILTER_NAME, "Ratio of N to alt exceeds specified ratio")); addFilterLine(new VCFFilterHeaderLine(ALLELE_FRACTION_FILTER_NAME, R))97 addFilterLine(new VCFFilterHeaderLine(ALLELE_FRACTION_FILTER_NAME, "Allele fraction is below specified threshold")); 98 99 //Mitochondrial M2-related filters addFilterLine(new VCFFilterHeaderLine(POSSIBLE_NUMT_FILTER_NAME, R))100 addFilterLine(new VCFFilterHeaderLine(POSSIBLE_NUMT_FILTER_NAME, "Allele depth is below expected coverage of NuMT in autosome")); addFilterLine(new VCFFilterHeaderLine(LOW_HET_FILTER_NAME, R))101 addFilterLine(new VCFFilterHeaderLine(LOW_HET_FILTER_NAME, "All low heteroplasmy sites are filtered when at least x low het sites pass all other filters")); addFilterLine(new VCFFilterHeaderLine(FAIL, R))102 addFilterLine(new VCFFilterHeaderLine(FAIL, "Fail the site if all alleles fail but for different reasons.")); addFilterLine(new VCFFilterHeaderLine(SITE_LEVEL_FILTERS, R))103 addFilterLine(new VCFFilterHeaderLine(SITE_LEVEL_FILTERS, "There are no allele specific filters that apply to this allele. Only site level filters apply.")); addFilterLine(new VCFFilterHeaderLine(LOW_HET_FILTER_NAME, R))104 addFilterLine(new VCFFilterHeaderLine(LOW_HET_FILTER_NAME, "All low heteroplasmy sites are filtered when at least x low het sites pass all other filters")); 105 addFormatLine(new VCFFormatHeaderLine(ALLELE_BALANCE_KEY, 1, VCFHeaderLineType.Float, R))106 addFormatLine(new VCFFormatHeaderLine(ALLELE_BALANCE_KEY, 1, VCFHeaderLineType.Float, "Allele balance for each het genotype")); addFormatLine(new VCFFormatHeaderLine(MAPPING_QUALITY_ZERO_BY_SAMPLE_KEY, 1, VCFHeaderLineType.Integer, R))107 addFormatLine(new VCFFormatHeaderLine(MAPPING_QUALITY_ZERO_BY_SAMPLE_KEY, 1, VCFHeaderLineType.Integer, "Number of Mapping Quality Zero Reads per sample")); addFormatLine(new VCFFormatHeaderLine(STRAND_COUNT_BY_SAMPLE_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, R))108 addFormatLine(new VCFFormatHeaderLine(STRAND_COUNT_BY_SAMPLE_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Number of reads on the forward and reverse strand supporting each allele (including reference)")); addFormatLine(new VCFFormatHeaderLine(STRAND_BIAS_BY_SAMPLE_KEY, 4, VCFHeaderLineType.Integer, R))109 addFormatLine(new VCFFormatHeaderLine(STRAND_BIAS_BY_SAMPLE_KEY, 4, VCFHeaderLineType.Integer, "Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.")); addFormatLine(new VCFFormatHeaderLine(HAPLOTYPE_CALLER_PHASING_ID_KEY, 1, VCFHeaderLineType.String, R))110 addFormatLine(new VCFFormatHeaderLine(HAPLOTYPE_CALLER_PHASING_ID_KEY, 1, VCFHeaderLineType.String, "Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group")); addFormatLine(new VCFFormatHeaderLine(HAPLOTYPE_CALLER_PHASING_GT_KEY, 1, VCFHeaderLineType.String, R))111 addFormatLine(new VCFFormatHeaderLine(HAPLOTYPE_CALLER_PHASING_GT_KEY, 1, VCFHeaderLineType.String, "Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles")); addFormatLine(new VCFFormatHeaderLine(MIN_DP_FORMAT_KEY, 1, VCFHeaderLineType.Integer, R))112 addFormatLine(new VCFFormatHeaderLine(MIN_DP_FORMAT_KEY, 1, VCFHeaderLineType.Integer, "Minimum DP observed within the GVCF block")); addFormatLine(new VCFFormatHeaderLine(REFERENCE_GENOTYPE_QUALITY, 1, VCFHeaderLineType.Integer, R))113 addFormatLine(new VCFFormatHeaderLine(REFERENCE_GENOTYPE_QUALITY, 1, VCFHeaderLineType.Integer, "Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)")); addFormatLine(new VCFFormatHeaderLine(TRANSMISSION_PROBABILITY_KEY, 1, VCFHeaderLineType.Integer, R))114 addFormatLine(new VCFFormatHeaderLine(TRANSMISSION_PROBABILITY_KEY, 1, VCFHeaderLineType.Integer, "Phred score of the genotype combination and phase given that the genotypes are correct")); addFormatLine(new VCFFormatHeaderLine(PHRED_SCALED_POSTERIORS_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, R))115 addFormatLine(new VCFFormatHeaderLine(PHRED_SCALED_POSTERIORS_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Phred-scaled Posterior Genotype Probabilities")); addFormatLine(new VCFFormatHeaderLine(JOINT_LIKELIHOOD_TAG_NAME, 1, VCFHeaderLineType.Integer, R))116 addFormatLine(new VCFFormatHeaderLine(JOINT_LIKELIHOOD_TAG_NAME, 1, VCFHeaderLineType.Integer, "Phred-scaled joint likelihood of the genotype combination (before applying family priors)")); addFormatLine(new VCFFormatHeaderLine(JOINT_POSTERIOR_TAG_NAME, 1, VCFHeaderLineType.Integer, R))117 addFormatLine(new VCFFormatHeaderLine(JOINT_POSTERIOR_TAG_NAME, 1, VCFHeaderLineType.Integer, "Phred-scaled joint posterior probability of the genotype combination (after applying family priors)")); 118 119 // M2-related format lines addFormatLine(new VCFFormatHeaderLine(ALLELE_FRACTION_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, R))120 addFormatLine(new VCFFormatHeaderLine(ALLELE_FRACTION_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele fractions of alternate alleles in the tumor")); addFormatLine(new VCFFormatHeaderLine(F1R2_KEY, VCFHeaderLineCount.R, VCFHeaderLineType.Integer, R))121 addFormatLine(new VCFFormatHeaderLine(F1R2_KEY, VCFHeaderLineCount.R, VCFHeaderLineType.Integer, "Count of reads in F1R2 pair orientation supporting each allele")); addFormatLine(new VCFFormatHeaderLine(F2R1_KEY, VCFHeaderLineCount.R, VCFHeaderLineType.Integer, R))122 addFormatLine(new VCFFormatHeaderLine(F2R1_KEY, VCFHeaderLineCount.R, VCFHeaderLineType.Integer, "Count of reads in F2R1 pair orientation supporting each allele")); 123 addInfoLine(new VCFInfoHeaderLine(MLE_ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, R))124 addInfoLine(new VCFInfoHeaderLine(MLE_ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed")); addInfoLine(new VCFInfoHeaderLine(MLE_ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, R))125 addInfoLine(new VCFInfoHeaderLine(MLE_ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed")); addInfoLine(new VCFInfoHeaderLine(DOWNSAMPLED_KEY, 0, VCFHeaderLineType.Flag, R))126 addInfoLine(new VCFInfoHeaderLine(DOWNSAMPLED_KEY, 0, VCFHeaderLineType.Flag, "Were any of the samples downsampled?")); addInfoLine(new VCFInfoHeaderLine(BASE_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, R))127 addInfoLine(new VCFInfoHeaderLine(BASE_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities")); addInfoLine(new VCFInfoHeaderLine(AS_BASE_QUAL_RANK_SUM_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, R))128 addInfoLine(new VCFInfoHeaderLine(AS_BASE_QUAL_RANK_SUM_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "allele specific Z-score from Wilcoxon rank sum test of each Alt Vs. Ref base qualities")); addInfoLine(new VCFInfoHeaderLine(AS_RAW_BASE_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.String, R))129 addInfoLine(new VCFInfoHeaderLine(AS_RAW_BASE_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.String, "raw data for allele specific rank sum test of base qualities")); addInfoLine(new VCFInfoHeaderLine(CLIPPING_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, R))130 addInfoLine(new VCFInfoHeaderLine(CLIPPING_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases")); addInfoLine(new VCFInfoHeaderLine(FISHER_STRAND_KEY, 1, VCFHeaderLineType.Float, R))131 addInfoLine(new VCFInfoHeaderLine(FISHER_STRAND_KEY, 1, VCFHeaderLineType.Float, "Phred-scaled p-value using Fisher's exact test to detect strand bias")); addInfoLine(new VCFInfoHeaderLine(AS_FISHER_STRAND_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, R))132 addInfoLine(new VCFInfoHeaderLine(AS_FISHER_STRAND_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "allele specific phred-scaled p-value using Fisher's exact test to detect strand bias of each alt allele")); addInfoLine(new VCFInfoHeaderLine(AS_SB_TABLE_KEY, 1, VCFHeaderLineType.String, R))133 addInfoLine(new VCFInfoHeaderLine(AS_SB_TABLE_KEY, 1, VCFHeaderLineType.String, "Allele-specific forward/reverse read counts for strand bias tests. Includes the reference and alleles separated by |.")); addInfoLine(new VCFInfoHeaderLine(NOCALL_CHROM_KEY, 1, VCFHeaderLineType.Integer, R))134 addInfoLine(new VCFInfoHeaderLine(NOCALL_CHROM_KEY, 1, VCFHeaderLineType.Integer, "Number of no-called samples")); addInfoLine(new VCFInfoHeaderLine(GQ_MEAN_KEY, 1, VCFHeaderLineType.Float, R))135 addInfoLine(new VCFInfoHeaderLine(GQ_MEAN_KEY, 1, VCFHeaderLineType.Float, "Mean of all GQ values")); addInfoLine(new VCFInfoHeaderLine(GQ_STDEV_KEY, 1, VCFHeaderLineType.Float, R))136 addInfoLine(new VCFInfoHeaderLine(GQ_STDEV_KEY, 1, VCFHeaderLineType.Float, "Standard deviation of all GQ values")); addInfoLine(new VCFInfoHeaderLine(HAPLOTYPE_SCORE_KEY, 1, VCFHeaderLineType.Float, R))137 addInfoLine(new VCFInfoHeaderLine(HAPLOTYPE_SCORE_KEY, 1, VCFHeaderLineType.Float, "Consistency of the site with at most two segregating haplotypes")); addInfoLine(new VCFInfoHeaderLine(INBREEDING_COEFFICIENT_KEY, 1, VCFHeaderLineType.Float, R))138 addInfoLine(new VCFInfoHeaderLine(INBREEDING_COEFFICIENT_KEY, 1, VCFHeaderLineType.Float, "Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation")); addInfoLine(new VCFInfoHeaderLine(AS_INBREEDING_COEFFICIENT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, R))139 addInfoLine(new VCFInfoHeaderLine(AS_INBREEDING_COEFFICIENT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele-specific inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation")); addInfoLine(new VCFInfoHeaderLine(EXCESS_HET_KEY, 1, VCFHeaderLineType.Float, R))140 addInfoLine(new VCFInfoHeaderLine(EXCESS_HET_KEY, 1, VCFHeaderLineType.Float, "Phred-scaled p-value for exact test of excess heterozygosity")); addInfoLine(new VCFInfoHeaderLine(RAW_GENOTYPE_COUNT_KEY, 3, VCFHeaderLineType.Integer, R))141 addInfoLine(new VCFInfoHeaderLine(RAW_GENOTYPE_COUNT_KEY, 3, VCFHeaderLineType.Integer, "Counts of genotypes w.r.t. the reference allele: 0/0, 0/*, */*, i.e. all alts lumped together; for use in calculating excess heterozygosity")); addInfoLine(new VCFInfoHeaderLine(LIKELIHOOD_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, R))142 addInfoLine(new VCFInfoHeaderLine(LIKELIHOOD_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt Vs. Ref haplotype likelihoods")); addInfoLine(new VCFInfoHeaderLine(MAP_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, R))143 addInfoLine(new VCFInfoHeaderLine(MAP_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities")); addInfoLine(new VCFInfoHeaderLine(AS_MAP_QUAL_RANK_SUM_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, R))144 addInfoLine(new VCFInfoHeaderLine(AS_MAP_QUAL_RANK_SUM_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "allele specific Z-score From Wilcoxon rank sum test of each Alt vs. Ref read mapping qualities")); addInfoLine(new VCFInfoHeaderLine(MAPPING_QUALITY_DEPTH_DEPRECATED, 1, VCFHeaderLineType.Integer, R + RAW_MAPPING_QUALITY_WITH_DEPTH_KEY + R))145 addInfoLine(new VCFInfoHeaderLine(MAPPING_QUALITY_DEPTH_DEPRECATED, 1, VCFHeaderLineType.Integer, "Depth over variant samples for better MQ calculation (deprecated -- use " + RAW_MAPPING_QUALITY_WITH_DEPTH_KEY + " instead.)")); addInfoLine(new VCFInfoHeaderLine(RAW_RMS_MAPPING_QUALITY_DEPRECATED, 1, VCFHeaderLineType.Float, R + RAW_MAPPING_QUALITY_WITH_DEPTH_KEY + R))146 addInfoLine(new VCFInfoHeaderLine(RAW_RMS_MAPPING_QUALITY_DEPRECATED, 1, VCFHeaderLineType.Float, "Raw data for RMS Mapping Quality (deprecated -- use " + RAW_MAPPING_QUALITY_WITH_DEPTH_KEY + " instead.)")); addInfoLine(new VCFInfoHeaderLine(RAW_MAPPING_QUALITY_WITH_DEPTH_KEY, 2, VCFHeaderLineType.Integer, R + RMSMappingQuality.getDeprecatedRawKeyName() + R))147 addInfoLine(new VCFInfoHeaderLine(RAW_MAPPING_QUALITY_WITH_DEPTH_KEY, 2, VCFHeaderLineType.Integer, "Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated " + RMSMappingQuality.getDeprecatedRawKeyName() + " formulation.")); addInfoLine(new VCFInfoHeaderLine(AS_RAW_RMS_MAPPING_QUALITY_KEY, 1, VCFHeaderLineType.String, R))148 addInfoLine(new VCFInfoHeaderLine(AS_RAW_RMS_MAPPING_QUALITY_KEY, 1, VCFHeaderLineType.String, "Allele-specfic raw data for RMS Mapping Quality")); addInfoLine(new VCFInfoHeaderLine(AS_RMS_MAPPING_QUALITY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, R))149 addInfoLine(new VCFInfoHeaderLine(AS_RMS_MAPPING_QUALITY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele-specific RMS Mapping Quality")); addInfoLine(new VCFInfoHeaderLine(AS_RAW_MAP_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.String, R))150 addInfoLine(new VCFInfoHeaderLine(AS_RAW_MAP_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.String, "Allele-specfic raw data for Mapping Quality Rank Sum")); addInfoLine(new VCFInfoHeaderLine(AS_MAP_QUAL_RANK_SUM_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, R))151 addInfoLine(new VCFInfoHeaderLine(AS_MAP_QUAL_RANK_SUM_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele-specific Mapping Quality Rank Sum")); addInfoLine(new VCFInfoHeaderLine(AS_FILTER_STATUS_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.String, R))152 addInfoLine(new VCFInfoHeaderLine(AS_FILTER_STATUS_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.String, "Filter status for each allele, as assessed by ApplyVQSR. Note that the VCF filter field will reflect the most lenient/sensitive status across all alleles.")); addInfoLine(new VCFInfoHeaderLine(AS_CULPRIT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.String, R))153 addInfoLine(new VCFInfoHeaderLine(AS_CULPRIT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.String, "For each alt allele, the annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out")); addInfoLine(new VCFInfoHeaderLine(AS_VQS_LOD_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.String, R))154 addInfoLine(new VCFInfoHeaderLine(AS_VQS_LOD_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.String, "For each alt allele, the log odds of being a true variant versus being false under the trained gaussian mixture model")); 155 addInfoLine(new VCFInfoHeaderLine(HI_CONF_DENOVO_KEY, 1, VCFHeaderLineType.String, R))156 addInfoLine(new VCFInfoHeaderLine(HI_CONF_DENOVO_KEY, 1, VCFHeaderLineType.String, "High confidence possible de novo mutation (GQ >= 20 for all trio members)=[comma-delimited list of child samples]")); addInfoLine(new VCFInfoHeaderLine(LO_CONF_DENOVO_KEY, 1, VCFHeaderLineType.String, R))157 addInfoLine(new VCFInfoHeaderLine(LO_CONF_DENOVO_KEY, 1, VCFHeaderLineType.String, "Low confidence possible de novo mutation (GQ >= 10 for child, GQ > 0 for parents)=[comma-delimited list of child samples]")); addInfoLine(new VCFInfoHeaderLine(QUAL_BY_DEPTH_KEY, 1, VCFHeaderLineType.Float, R))158 addInfoLine(new VCFInfoHeaderLine(QUAL_BY_DEPTH_KEY, 1, VCFHeaderLineType.Float, "Variant Confidence/Quality by Depth")); addInfoLine(new VCFInfoHeaderLine(AS_QUAL_BY_DEPTH_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, R))159 addInfoLine(new VCFInfoHeaderLine(AS_QUAL_BY_DEPTH_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele-specific Variant Confidence/Quality by Depth")); addInfoLine(new VCFInfoHeaderLine(AS_QUAL_KEY, 1, VCFHeaderLineType.Float, R))160 addInfoLine(new VCFInfoHeaderLine(AS_QUAL_KEY, 1, VCFHeaderLineType.Float, "Allele-specific Variant Qual Score")); addInfoLine(new VCFInfoHeaderLine(AS_RAW_QUAL_APPROX_KEY, 1, VCFHeaderLineType.String, R))161 addInfoLine(new VCFInfoHeaderLine(AS_RAW_QUAL_APPROX_KEY, 1, VCFHeaderLineType.String, "Allele-specific Variant Qual approximation")); addInfoLine(new VCFInfoHeaderLine(RAW_QUAL_APPROX_KEY, 1, VCFHeaderLineType.Integer, R))162 addInfoLine(new VCFInfoHeaderLine(RAW_QUAL_APPROX_KEY, 1, VCFHeaderLineType.Integer, "Sum of PL[0] values; used to approximate the QUAL score")); addInfoLine(new VCFInfoHeaderLine(AS_RAW_QUAL_APPROX_KEY, 1, VCFHeaderLineType.String, R))163 addInfoLine(new VCFInfoHeaderLine(AS_RAW_QUAL_APPROX_KEY, 1, VCFHeaderLineType.String, "Allele-specific QUAL approximations")); addInfoLine(new VCFInfoHeaderLine(VARIANT_DEPTH_KEY, 1, VCFHeaderLineType.Integer, R))164 addInfoLine(new VCFInfoHeaderLine(VARIANT_DEPTH_KEY, 1, VCFHeaderLineType.Integer, "(informative) depth over variant genotypes")); addInfoLine(new VCFInfoHeaderLine(AS_VARIANT_DEPTH_KEY, 1, VCFHeaderLineType.String, R))165 addInfoLine(new VCFInfoHeaderLine(AS_VARIANT_DEPTH_KEY, 1, VCFHeaderLineType.String, "Allele-specific (informative) depth over variant genotypes -- including ref, RAW format")); addInfoLine(new VCFInfoHeaderLine(AS_ALT_ALLELE_DEPTH_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, R))166 addInfoLine(new VCFInfoHeaderLine(AS_ALT_ALLELE_DEPTH_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Allele-specific (informative) depth for alt alleles over variant genotypes; effectively sum of ADs")); addInfoLine(new VCFInfoHeaderLine(READ_POS_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, R))167 addInfoLine(new VCFInfoHeaderLine(READ_POS_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias")); addInfoLine(new VCFInfoHeaderLine(AS_READ_POS_RANK_SUM_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, R))168 addInfoLine(new VCFInfoHeaderLine(AS_READ_POS_RANK_SUM_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "allele specific Z-score from Wilcoxon rank sum test of each Alt vs. Ref read position bias")); addInfoLine(new VCFInfoHeaderLine(AS_RAW_READ_POS_RANK_SUM_KEY, 1, VCFHeaderLineType.String, R))169 addInfoLine(new VCFInfoHeaderLine(AS_RAW_READ_POS_RANK_SUM_KEY, 1, VCFHeaderLineType.String, "allele specific raw data for rank sum test of read position bias")); addInfoLine(new VCFInfoHeaderLine(SAMPLE_LIST_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, R))170 addInfoLine(new VCFInfoHeaderLine(SAMPLE_LIST_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "List of polymorphic samples")); addInfoLine(new VCFInfoHeaderLine(STRAND_ODDS_RATIO_KEY, 1, VCFHeaderLineType.Float, R))171 addInfoLine(new VCFInfoHeaderLine(STRAND_ODDS_RATIO_KEY, 1, VCFHeaderLineType.Float, "Symmetric Odds Ratio of 2x2 contingency table to detect strand bias")); addInfoLine(new VCFInfoHeaderLine(AS_STRAND_ODDS_RATIO_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, R))172 addInfoLine(new VCFInfoHeaderLine(AS_STRAND_ODDS_RATIO_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele specific strand Odds Ratio of 2x|Alts| contingency table to detect allele specific strand bias")); addInfoLine(new VCFInfoHeaderLine(STR_PRESENT_KEY, 0, VCFHeaderLineType.Flag, R))173 addInfoLine(new VCFInfoHeaderLine(STR_PRESENT_KEY, 0, VCFHeaderLineType.Flag, "Variant is a short tandem repeat")); addInfoLine(new VCFInfoHeaderLine(REPEAT_UNIT_KEY, 1, VCFHeaderLineType.String, R))174 addInfoLine(new VCFInfoHeaderLine(REPEAT_UNIT_KEY, 1, VCFHeaderLineType.String, "Tandem repeat unit (bases)")); addInfoLine(new VCFInfoHeaderLine(REPEATS_PER_ALLELE_KEY, VCFHeaderLineCount.R, VCFHeaderLineType.Integer, R))175 addInfoLine(new VCFInfoHeaderLine(REPEATS_PER_ALLELE_KEY, VCFHeaderLineCount.R, VCFHeaderLineType.Integer, "Number of times tandem repeat unit is repeated, for each allele (including reference)")); addInfoLine(new VCFInfoHeaderLine(NUMBER_OF_DISCOVERED_ALLELES_KEY, 1, VCFHeaderLineType.Integer, R))176 addInfoLine(new VCFInfoHeaderLine(NUMBER_OF_DISCOVERED_ALLELES_KEY, 1, VCFHeaderLineType.Integer, "Number of alternate alleles discovered (but not necessarily genotyped) at this site")); addInfoLine(new VCFInfoHeaderLine(ORIGINAL_AC_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, R))177 addInfoLine(new VCFInfoHeaderLine(ORIGINAL_AC_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Original AC")); addInfoLine(new VCFInfoHeaderLine(ORIGINAL_AF_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, R))178 addInfoLine(new VCFInfoHeaderLine(ORIGINAL_AF_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Original AF")); addInfoLine(new VCFInfoHeaderLine(ORIGINAL_AN_KEY, 1, VCFHeaderLineType.Integer, R))179 addInfoLine(new VCFInfoHeaderLine(ORIGINAL_AN_KEY, 1, VCFHeaderLineType.Integer, "Original AN")); addInfoLine(new VCFInfoHeaderLine(ORIGINAL_DP_KEY, 1, VCFHeaderLineType.Integer, R))180 addInfoLine(new VCFInfoHeaderLine(ORIGINAL_DP_KEY, 1, VCFHeaderLineType.Integer, "Original DP")); addInfoLine(new VCFInfoHeaderLine(VQS_LOD_KEY, 1, VCFHeaderLineType.Float, R))181 addInfoLine(new VCFInfoHeaderLine(VQS_LOD_KEY, 1, VCFHeaderLineType.Float, "Log odds of being a true variant versus being false under the trained gaussian mixture model")); addInfoLine(new VCFInfoHeaderLine(CNN_1D_KEY, 1, VCFHeaderLineType.Float, R))182 addInfoLine(new VCFInfoHeaderLine(CNN_1D_KEY, 1, VCFHeaderLineType.Float, "Log odds of being a true variant versus being false under the trained 1D Convolutional Neural Network")); addInfoLine(new VCFInfoHeaderLine(CNN_2D_KEY, 1, VCFHeaderLineType.Float, R))183 addInfoLine(new VCFInfoHeaderLine(CNN_2D_KEY, 1, VCFHeaderLineType.Float, "Log odds of being a true variant versus being false under the trained 2D Convolutional Neural Network")); addInfoLine(new VCFInfoHeaderLine(CULPRIT_KEY, 1, VCFHeaderLineType.String, R))184 addInfoLine(new VCFInfoHeaderLine(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")); addInfoLine(new VCFInfoHeaderLine(POSITIVE_LABEL_KEY, 1, VCFHeaderLineType.Flag, R))185 addInfoLine(new VCFInfoHeaderLine(POSITIVE_LABEL_KEY, 1, VCFHeaderLineType.Flag, "This variant was used to build the positive training set of good variants")); addInfoLine(new VCFInfoHeaderLine(NEGATIVE_LABEL_KEY, 1, VCFHeaderLineType.Flag, R))186 addInfoLine(new VCFInfoHeaderLine(NEGATIVE_LABEL_KEY, 1, VCFHeaderLineType.Flag, "This variant was used to build the negative training set of bad variants")); addInfoLine(new VCFInfoHeaderLine(GENOTYPE_AND_VALIDATE_STATUS_KEY, 1, VCFHeaderLineType.String, R))187 addInfoLine(new VCFInfoHeaderLine(GENOTYPE_AND_VALIDATE_STATUS_KEY, 1, VCFHeaderLineType.String, "Value from the validation VCF")); addInfoLine(new VCFInfoHeaderLine(INTERVAL_GC_CONTENT_KEY, 1, VCFHeaderLineType.Float, R))188 addInfoLine(new VCFInfoHeaderLine(INTERVAL_GC_CONTENT_KEY, 1, VCFHeaderLineType.Float, "GC Content of the interval")); addInfoLine(new VCFInfoHeaderLine(GENOTYPE_PRIOR_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, R))189 addInfoLine(new VCFInfoHeaderLine(GENOTYPE_PRIOR_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Genotype Likelihood Prior")); 190 191 // M2-related info lines addInfoLine(new VCFInfoHeaderLine(EVENT_COUNT_IN_HAPLOTYPE_KEY, 1, VCFHeaderLineType.Integer, R))192 addInfoLine(new VCFInfoHeaderLine(EVENT_COUNT_IN_HAPLOTYPE_KEY, 1, VCFHeaderLineType.Integer, "Number of events in this haplotype")); addInfoLine(new VCFInfoHeaderLine(NORMAL_LOG_10_ODDS_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, R))193 addInfoLine(new VCFInfoHeaderLine(NORMAL_LOG_10_ODDS_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Normal log 10 likelihood ratio of diploid het or hom alt genotypes")); addInfoLine(new VCFInfoHeaderLine(TUMOR_LOG_10_ODDS_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, R))194 addInfoLine(new VCFInfoHeaderLine(TUMOR_LOG_10_ODDS_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Log 10 likelihood ratio score of variant existing versus not existing")); addFormatLine(new VCFFormatHeaderLine(TUMOR_LOG_10_ODDS_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, R))195 addFormatLine(new VCFFormatHeaderLine(TUMOR_LOG_10_ODDS_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Log 10 likelihood ratio score of variant existing versus not existing")); addInfoLine(new VCFInfoHeaderLine(IN_PON_KEY, 0, VCFHeaderLineType.Flag, R))196 addInfoLine(new VCFInfoHeaderLine(IN_PON_KEY, 0, VCFHeaderLineType.Flag, "site found in panel of normals")); addInfoLine(new VCFInfoHeaderLine(POPULATION_AF_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, R))197 addInfoLine(new VCFInfoHeaderLine(POPULATION_AF_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "negative log 10 population allele frequencies of alt alleles")); addInfoLine(new VCFInfoHeaderLine(GERMLINE_QUAL_KEY, 1, VCFHeaderLineType.Integer, R))198 addInfoLine(new VCFInfoHeaderLine(GERMLINE_QUAL_KEY, 1, VCFHeaderLineType.Integer, "Phred-scaled quality that alt alleles are not germline variants")); addInfoLine(new VCFInfoHeaderLine(SEQUENCING_QUAL_KEY, 1, VCFHeaderLineType.Integer, R))199 addInfoLine(new VCFInfoHeaderLine(SEQUENCING_QUAL_KEY, 1, VCFHeaderLineType.Integer, "Phred-scaled quality that alt alleles are not sequencing errors")); addInfoLine(new VCFInfoHeaderLine(POLYMERASE_SLIPPAGE_QUAL_KEY, 1, VCFHeaderLineType.Integer, R))200 addInfoLine(new VCFInfoHeaderLine(POLYMERASE_SLIPPAGE_QUAL_KEY, 1, VCFHeaderLineType.Integer, "Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors")); addInfoLine(new VCFInfoHeaderLine(STRAND_QUAL_KEY, 1, VCFHeaderLineType.Integer, R))201 addInfoLine(new VCFInfoHeaderLine(STRAND_QUAL_KEY, 1, VCFHeaderLineType.Integer, "Phred-scaled quality of strand bias artifact")); addInfoLine(new VCFInfoHeaderLine(CONTAMINATION_QUAL_KEY, 1, VCFHeaderLineType.Float, R))202 addInfoLine(new VCFInfoHeaderLine(CONTAMINATION_QUAL_KEY, 1, VCFHeaderLineType.Float, "Phred-scaled qualities that alt allele are not due to contamination")); addInfoLine(new VCFInfoHeaderLine(READ_ORIENTATION_QUAL_KEY, 1, VCFHeaderLineType.Float, R))203 addInfoLine(new VCFInfoHeaderLine(READ_ORIENTATION_QUAL_KEY, 1, VCFHeaderLineType.Float, "Phred-scaled qualities that alt allele are not due to read orientation artifact")); addInfoLine(new VCFInfoHeaderLine(NORMAL_ARTIFACT_LOG_10_ODDS_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, R))204 addInfoLine(new VCFInfoHeaderLine(NORMAL_ARTIFACT_LOG_10_ODDS_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Negative log 10 odds of artifact in normal with same allele fraction as tumor")); addInfoLine(new VCFInfoHeaderLine(ORIGINAL_CONTIG_MISMATCH_KEY, 1, VCFHeaderLineType.Integer, R))205 addInfoLine(new VCFInfoHeaderLine(ORIGINAL_CONTIG_MISMATCH_KEY, 1, VCFHeaderLineType.Integer, "Number of alt reads whose original alignment doesn't match the current contig.")); addInfoLine(new VCFInfoHeaderLine(N_COUNT_KEY, 1, VCFHeaderLineType.Integer, R))206 addInfoLine(new VCFInfoHeaderLine(N_COUNT_KEY, 1, VCFHeaderLineType.Integer, "Count of N bases in the pileup")); addInfoLine(new VCFInfoHeaderLine(AS_UNIQUE_ALT_READ_SET_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, R))207 addInfoLine(new VCFInfoHeaderLine(AS_UNIQUE_ALT_READ_SET_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Number of reads with unique start and mate end positions for each alt at a variant site")); addInfoLine(new BaseQuality().getDescriptions().get(0))208 addInfoLine(new BaseQuality().getDescriptions().get(0)); addInfoLine(new FragmentLength().getDescriptions().get(0))209 addInfoLine(new FragmentLength().getDescriptions().get(0)); addInfoLine(new MappingQuality().getDescriptions().get(0))210 addInfoLine(new MappingQuality().getDescriptions().get(0)); addInfoLine(new ReadPosition().getDescriptions().get(0))211 addInfoLine(new ReadPosition().getDescriptions().get(0)); addInfoLine(new AS_StrandBiasMutectAnnotation().getDescriptions().get(0))212 addInfoLine(new AS_StrandBiasMutectAnnotation().getDescriptions().get(0)); addInfoLine(new VCFInfoHeaderLine(UNITIG_SIZES_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, R))213 addInfoLine(new VCFInfoHeaderLine(UNITIG_SIZES_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Sizes of reassembled unitigs")); addInfoLine(new VCFInfoHeaderLine(JOINT_ALIGNMENT_COUNT_KEY, 1, VCFHeaderLineType.Integer, R))214 addInfoLine(new VCFInfoHeaderLine(JOINT_ALIGNMENT_COUNT_KEY, 1, VCFHeaderLineType.Integer, "Number of joint alignments")); addInfoLine(new VCFInfoHeaderLine(ALIGNMENT_SCORE_DIFFERENCE_KEY, 1, VCFHeaderLineType.Integer, R))215 addInfoLine(new VCFInfoHeaderLine(ALIGNMENT_SCORE_DIFFERENCE_KEY, 1, VCFHeaderLineType.Integer, "Difference in alignment score between best and next-best alignment")); 216 } 217 } 218