Package htsjdk.variant.vcf

Examples of htsjdk.variant.vcf.VCFFilterHeaderLine

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        final List<String> inputNames = Arrays.asList(validation.getName());

        // setup the header fields
        Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
        hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames));
        hInfo.add(new VCFFilterHeaderLine("bootstrap","This site used for genotype bootstrapping with ProduceBeagleInputWalker"));

        bootstrapVCFOutput.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames)));
    }
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        final VCFFileReader in = new VCFFileReader(INPUT, false);
        final FilterApplyingVariantIterator iterator = new FilterApplyingVariantIterator(in.iterator(), variantFilters, genotypeFilters);

        final VariantContextWriter out = new VariantContextWriterBuilder().setOutputFile(OUTPUT).build();
        final VCFHeader header = in.getFileHeader();
        header.addMetaDataLine(new VCFFilterHeaderLine("AllGtsFiltered", "Site filtered out because all genotypes are filtered out."));
        header.addMetaDataLine(new VCFFormatHeaderLine("FT", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Genotype filters."));
        for (final VariantFilter filter : variantFilters) {
            for (final VCFFilterHeaderLine line : filter.headerLines()) {
                header.addMetaDataLine(line);
            }
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        this.maxPhredScalePValue= maxPhredScalePValue;
    }

    @Override
    public List<VCFFilterHeaderLine> headerLines() {
        return CollectionUtil.makeList(new VCFFilterHeaderLine("StrandBias", "Site exhibits excessive allele/strand correlation."));
    }
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        }
    }

    @Override
    public List<VCFFilterHeaderLine> headerLines() {
        return CollectionUtil.makeList(new VCFFilterHeaderLine(FILTER_NAME, "Site exhibits QD value below a hard limit."));
    }
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    private static class Counts { int samples; int allele1; int allele2; }

    @Override
    public List<VCFFilterHeaderLine> headerLines() {
        return CollectionUtil.makeList(new VCFFilterHeaderLine(AB_FILTER, "Heterozygote allele balance below required threshold."));
    }
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Related Classes of htsjdk.variant.vcf.VCFFilterHeaderLine

  • org.broadinstitute.gatk.tools.walkers.beagle.ProduceBeagleInput
  • picard.vcf.filter.AlleleBalanceFilter
  • picard.vcf.filter.FilterVcf
  • picard.vcf.filter.FisherStrandFilter
  • picard.vcf.filter.QdFilter
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