Examples with WellformedReadFilter org.broadinstitute.hellbender.engine.filters.WellformedReadFilter used on opensource projects

Example 11 with WellformedReadFilter

use of org.broadinstitute.hellbender.engine.filters.WellformedReadFilter in project gatk by broadinstitute.

the class HaplotypeCallerEngine method makeStandardHCReadFilters.

/**
     * @return the default set of read filters for use with the HaplotypeCaller
     */
public static List<ReadFilter> makeStandardHCReadFilters() {
    List<ReadFilter> filters = new ArrayList<>();
    filters.add(new MappingQualityReadFilter(READ_QUALITY_FILTER_THRESHOLD));
    filters.add(ReadFilterLibrary.MAPPING_QUALITY_AVAILABLE);
    filters.add(ReadFilterLibrary.MAPPED);
    filters.add(ReadFilterLibrary.PRIMARY_ALIGNMENT);
    filters.add(ReadFilterLibrary.NOT_DUPLICATE);
    filters.add(ReadFilterLibrary.PASSES_VENDOR_QUALITY_CHECK);
    filters.add(ReadFilterLibrary.NON_ZERO_REFERENCE_LENGTH_ALIGNMENT);
    filters.add(ReadFilterLibrary.GOOD_CIGAR);
    filters.add(new WellformedReadFilter());
    return filters;
}

Example 12 with WellformedReadFilter

use of org.broadinstitute.hellbender.engine.filters.WellformedReadFilter in project gatk by broadinstitute.

the class Mutect2Engine method makeStandardMutect2ReadFilters.

/**
     * @return the default set of read filters for use with Mutect2
     */
public static List<ReadFilter> makeStandardMutect2ReadFilters() {
    // The order in which we apply filters is important. Cheap filters come first so we fail fast
    List<ReadFilter> filters = new ArrayList<>();
    filters.add(new MappingQualityReadFilter(READ_QUALITY_FILTER_THRESHOLD));
    filters.add(ReadFilterLibrary.MAPPING_QUALITY_AVAILABLE);
    filters.add(ReadFilterLibrary.MAPPING_QUALITY_NOT_ZERO);
    filters.add(ReadFilterLibrary.MAPPED);
    filters.add(ReadFilterLibrary.PRIMARY_ALIGNMENT);
    filters.add(ReadFilterLibrary.NOT_DUPLICATE);
    filters.add(ReadFilterLibrary.PASSES_VENDOR_QUALITY_CHECK);
    filters.add(ReadFilterLibrary.NON_ZERO_REFERENCE_LENGTH_ALIGNMENT);
    filters.add(GOOD_READ_LENGTH_FILTER);
    filters.add(ReadFilterLibrary.MATE_ON_SAME_CONTIG_OR_NO_MAPPED_MATE);
    filters.add(ReadFilterLibrary.GOOD_CIGAR);
    filters.add(new WellformedReadFilter());
    return filters;
}