Package htsjdk.variant.vcf

Examples of htsjdk.variant.vcf.VCFInfoHeaderLine

87
88
89
90
91
92
93
    @Override
    public List<String> getKeyNames() { return Arrays.asList("ReadPosRankSum"); }

    @Override
    public List<VCFInfoHeaderLine> getDescriptions() {
        return Arrays.asList(new VCFInfoHeaderLine("ReadPosRankSum", 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"));
    }
View Full Code Here
116
117
118
119
120
121
122
123
124
125
126
127
    }

    @Override
    public List<VCFInfoHeaderLine> getDescriptions() {
        return Arrays.asList(
                new VCFInfoHeaderLine(CCC, 1, VCFHeaderLineType.Integer, "Number of called chromosomes"),
                new VCFInfoHeaderLine(NCC, 1, VCFHeaderLineType.Integer, "Number of no-called samples"),
                new VCFInfoHeaderLine(HWP, 1, VCFHeaderLineType.Float, "P value from test of Hardy Weinberg Equilibrium"),
                new VCFInfoHeaderLine(GQ_MEAN, 1, VCFHeaderLineType.Float, "Mean of all GQ values"),
                new VCFInfoHeaderLine(GQ_STDDEV, 1, VCFHeaderLineType.Float, "Standard deviation of all GQ values")
        );
    }
View Full Code Here
76
77
78
79
80
81
public class BaseQualityRankSumTest extends RankSumTest implements StandardAnnotation {
    @Override
    public List<String> getKeyNames() { return Arrays.asList("BaseQRankSum"); }

    @Override
    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("BaseQRankSum", 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities")); }
View Full Code Here
137
138
139
140
141
142
        return map;
    }

    public List<String> getKeyNames() { return Arrays.asList("HW"); }

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("HW", 1, VCFHeaderLineType.Float, "Phred-scaled p-value for Hardy-Weinberg violation")); }
View Full Code Here
153
154
155
156
157
158
159
    }

    // return the descriptions used for the VCF INFO meta field
    public List<String> getKeyNames() { return Arrays.asList(HI_CONF_DENOVO_KEY,LO_CONF_DENOVO_KEY); }

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(HI_CONF_DENOVO_KEY, 1, VCFHeaderLineType.String, "High confidence possible de novo mutation (GQ >= "+hi_GQ_threshold+" for all trio members)=[comma-delimited list of child samples]"),
            new VCFInfoHeaderLine(LO_CONF_DENOVO_KEY, 1, VCFHeaderLineType.String, "Low confidence possible de novo mutation (GQ >= "+lo_GQ_threshold+" for child, GQ > 0 for parents)=[comma-delimited list of child samples]")); }
View Full Code Here
74
75
76
77
78
79
public class ClippingRankSumTest extends RankSumTest {
    @Override
    public List<String> getKeyNames() { return Arrays.asList("ClippingRankSum"); }

    @Override
    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("ClippingRankSum", 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases")); }
View Full Code Here
101
102
103
104
105
106
        return map;
    }

    public List<String> getKeyNames() { return Arrays.asList("Samples"); }

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("Samples", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "List of polymorphic samples")); }
View Full Code Here
81
82
83
84
85
86
public class MappingQualityRankSumTest extends RankSumTest implements StandardAnnotation {
    @Override
    public List<String> getKeyNames() { return Arrays.asList("MQRankSum"); }

    @Override
    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("MQRankSum", 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities")); }
View Full Code Here
178
179
180
181
182
183
184
185
186
187
188
189
            STATUS_KEY = null;

        // for now, INFO and FORMAT fields are not propagated to the output VCF (so they aren't put into the header)
        Set<VCFHeaderLine> headerLines = new HashSet<VCFHeaderLine>();
        if ( SET_KEY != null )
            headerLines.add(new VCFInfoHeaderLine(SET_KEY, 1, VCFHeaderLineType.String, "Source VCF for the merged record"));
        if ( STATUS_KEY != null )
            headerLines.add(new VCFInfoHeaderLine(STATUS_KEY, 1, VCFHeaderLineType.String, "Extent to which records match"));
        final VCFHeader vcfHeader = new VCFHeader(headerLines, Collections.<String>emptySet());
        baseWriter.writeHeader(vcfHeader);
        writer = VariantContextWriterFactory.sortOnTheFly(baseWriter, ACTIVE_WINDOW);
    }
View Full Code Here
155
156
157
158
159
160
161
162
    }

    public Set<VCFInfoHeaderLine> getAppropriateVCFInfoHeaders() {
        Set<VCFInfoHeaderLine> headerInfo = new HashSet<>();
        if ( configuration.genotypeArgs.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED )
            headerInfo.add(new VCFInfoHeaderLine(UnifiedGenotypingEngine.NUMBER_OF_DISCOVERED_ALLELES_KEY, 1, VCFHeaderLineType.Integer, "Number of alternate alleles discovered (but not necessarily genotyped) at this site"));
        return headerInfo;
    }
View Full Code Here
TOP

Related Classes of htsjdk.variant.vcf.VCFInfoHeaderLine

  • bcbio.gatk.tools.walkers.annotator.FisherStrand
  • bcbio.gatk.tools.walkers.annotator.GCContent
  • bcbio.variation.annotate.AlleleBalanceConfidenceInterval
  • bcbio.variation.annotate.MostProbableGenotype
  • bcbio.variation.annotate.ReadMeanLen
  • bcbio.variation.annotate.ReadMeanPos
  • bcbio.variation.annotate.ReadPosEndDist
  • org.broad.igv.variant.vcf.VCFWriterTest
  • org.broadinstitute.gatk.tools.walkers.annotator.AlleleBalance
  • org.broadinstitute.gatk.tools.walkers.annotator.BaseCounts
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.