AlignmentAgreesWithHeaderReadFilter

Filters out reads where the alignment does not match the contents of the header

AllowAllReadsReadFilter

Do not filter out any read

AmbiguousBaseReadFilter

Filters out reads that have greater than the threshold number of N bases

CigarContainsNoNOperator

Filter out reads with CIGAR containing N operator

FirstOfPairReadFilter

Keep only reads that are first of pair

FragmentLengthReadFilter

Keep only read pairs with insert length less than or equal to the given value

GoodCigarReadFilter

Keep only reads containing good CIGAR string

HasReadGroupReadFilter

Filter out reads without Read Group

LibraryReadFilter

Keep only reads from the specified library

MappedReadFilter

Filter out unmapped reads

MappingQualityAvailableReadFilter

Filter out reads without available mapping quality

MappingQualityNotZeroReadFilter

Filter out reads with mapping quality equal to zero

MappingQualityReadFilter

Keep only reads with mapping qualities within a specified range

MatchingBasesAndQualsReadFilter

Filter out reads where the bases and qualities do not match

MateDifferentStrandReadFilter

Keep only reads with mates mapped on the different strand

MateOnSameContigOrNoMappedMateReadFilter

Keep only reads whose mate maps to the same contig or is unmapped

MetricsReadFilter

Filter out reads that fail platform quality checks, are unmapped and represent secondary/supplementary alignments

NonZeroFragmentLengthReadFilter

Filter out reads with fragment length different from zero

NonZeroReferenceLengthAlignmentReadFilter

Filter out reads that do not align to the reference

NotDuplicateReadFilter

Filter out reads marked as duplicate

NotSecondaryAlignmentReadFilter

Filter out reads representing secondary alignments

NotSupplementaryAlignmentReadFilter

Filter out reads representing supplementary alignments

OverclippedReadFilter

Filter out reads that are over-soft-clipped

PairedReadFilter

Filter out unpaired reads

PassesVendorQualityCheckReadFilter

Filter out reads failing platfor/vendor quality checks

PlatformReadFilter

Keep only reads with matching Read Group platform

PlatformUnitReadFilter

Filter out reads with matching platform unit attribute

PrimaryLineReadFilter

Keep only reads representing primary alignments (those that satisfy both the NotSecondaryAlignment and NotSupplementaryAlignment filters, or in terms of SAM flag values, must have neither of the 0x100 or 0x800 flags set).

ProperlyPairedReadFilter

Keep only reads that are properly paired

ReadGroupBlackListReadFilter

Keep records not matching the read group tag and exact match string.

ReadGroupReadFilter

Keep only reads from the specified read group

ReadLengthEqualsCigarLengthReadFilter

Filter out reads where the read and CIGAR do not match in length

ReadLengthReadFilter

Keep only reads whose length is within a certain range

ReadNameReadFilter

Keep only reads with this read name

ReadStrandFilter

Keep only reads whose strand is as specified

SampleReadFilter

Keep only reads for a given sample

SecondOfPairReadFilter

Keep only paired reads that are second of pair

SeqIsStoredReadFilter

Keep only reads with sequenced bases

ValidAlignmentEndReadFilter

Keep only reads where the read end is properly aligned

ValidAlignmentStartReadFilter

Keep only reads with a valid alignment start

WellformedReadFilter

Keep only reads that are well-formed