AlignmentAgreesWithHeaderReadFilter	AlignmentAgreesWithHeaderReadFilter	Filters out reads where the alignment does not match the contents of the header. The read does not match the contents of the header if: It is aligned to a non-existing contig, or It is aligned to a point after the end of the contig
AllowAllReadsReadFilter	AllowAllReadsReadFilter	Do not filter out any read.
AmbiguousBaseReadFilter	AmbiguousBaseReadFilter	Filters out reads that have greater than the threshold number for unknown (N) bases.
CigarContainsNoNOperator	CigarContainsNoNOperator	Filter out reads containing skipped region from the reference (CIGAR strings with 'N' operator).
FirstOfPairReadFilter	FirstOfPairReadFilter	Keep only reads that are first of pair (0x1 and 0x40). 
FragmentLengthReadFilter	FragmentLengthReadFilter	Keep only read pairs with insert length less than or equal to the given value
GoodCigarReadFilter	GoodCigarReadFilter	Keep only reads containing good CIGAR string. Good CIGAR strings have the following properties: Valid according to the SAM specifications, Does not start or end with deletions (with or without preceding clips), and Does not have consecutive deletion/insertion operators.
HasReadGroupReadFilter	HasReadGroupReadFilter	Filter out reads without the SAM record RG (Read Group) tag. 
IntervalOverlapReadFilter	IntervalOverlapReadFilter	Filters out reads that don't overlap the specified region. NOTE: This approach to extracting overlapping reads is very slow compared to using PrintReads and -L (intervals) on an indexed bam file.
LibraryReadFilter	LibraryReadFilter	Filters out reads that don't overlap the specified region. NOTE: This approach to extracting overlapping reads is very slow compared to using PrintReads and -L (intervals) on an indexed bam file.
MappedReadFilter	MappedReadFilter	Filter out unmapped reads. Unmapped reads are defined by three criteria:  SAM flag value 0x4, An asterisk for reference name or RNAME (column 3 of a SAM record), or A zero value for leftmost mapping position for POS (column 4 of SAM record).
MappingQualityAvailableReadFilter	MappingQualityAvailableReadFilter	Filter out reads without available mapping quality (MAPQ=255). 
MappingQualityNotZeroReadFilter	MappingQualityNotZeroReadFilter	Filter out reads with mapping quality equal to zero
MappingQualityReadFilter	MappingQualityReadFilter	Keep only reads with mapping qualities within a specified range.
MatchingBasesAndQualsReadFilter	MatchingBasesAndQualsReadFilter	Filter out reads where the bases and qualities do not match in length. 
MateDifferentStrandReadFilter	MateDifferentStrandReadFilter	Keep only reads with mates mapped on the different strand.  For paired reads (0x1), keep only reads that are mapped, have a mate that is mapped (read is not 0x8), and both the read and its mate are on different strands (when read is 0x20, it is not 0x10), as is the typical case.
MateOnSameContigOrNoMappedMateReadFilter	MateOnSameContigOrNoMappedMateReadFilter	"Keep only reads that have a mate that maps to the same contig (RNEXT is ""=""), is single ended (not 0x1) or has an unmapped mate (0x8). "
MateUnmappedAndUnmappedReadFilter	MateUnmappedAndUnmappedReadFilter	Filters reads whose mate is unmapped as well as unmapped reads.
MetricsReadFilter	MetricsReadFilter	Filter out reads that fail platform quality checks, are unmapped and represent secondary/supplementary alignments.
NonChimericOriginalAlignmentReadFilter	NonChimericOriginalAlignmentReadFilter	Filters reads whose original alignment was chimeric.
NonZeroFragmentLengthReadFilter	NonZeroFragmentLengthReadFilter	Filter out reads with fragment length (insert size) different from zero. 
NonZeroReferenceLengthAlignmentReadFilter	NonZeroReferenceLengthAlignmentReadFilter	Filter out reads that do not align to the reference. Filter interprets each of the CIGAR operators M, D, N, = and X as alignment.
NotDuplicateReadFilter	NotDuplicateReadFilter	Filter out reads marked as duplicate (0x400). 
NotSecondaryAlignmentReadFilter	NotSecondaryAlignmentReadFilter	Filter out reads representing secondary alignments (0x100). 
NotSupplementaryAlignmentReadFilter	NotSupplementaryAlignmentReadFilter	Filter out reads representing supplementary alignments (0x800). 
OverclippedReadFilter	OverclippedReadFilter	Filter out reads where the number of bases without soft-clips (M, I, X, and = CIGAR operators) is lower than a threshold. This filter is intended to filter out reads that are potentially from foreign organisms. From experience with sequencing of human DNA we have found cases of contamination by bacterial organisms; the symptoms of such contamination are a class of reads with only a small number of aligned bases and additionally many soft-clipped bases. This filter is intended to remove such reads.
PairedReadFilter	PairedReadFilter	Filter out unpaired reads (not 0x1). 
PassesVendorQualityCheckReadFilter	PassesVendorQualityCheckReadFilter	Filter out reads failing platform/vendor quality checks (0x200). 
PlatformReadFilter	PlatformReadFilter	Keep only reads where the the Read Group platform attribute (RG:PL tag) contains the given string. Note: Matching is done by case-insensitive substring matching.
PlatformUnitReadFilter	PlatformUnitReadFilter	Filter out reads where the the platform unit attribute (PU tag) contains the given string. Note: Matching is done by exact case-sensitive text matching.
PrimaryLineReadFilter	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	ProperlyPairedReadFilter	Keep only paired reads that are properly paired (0x1 and 0x2). Removes single ended reads. 
ReadGroupBlackListReadFilter	ReadGroupBlackListReadFilter	Keep records not matching the read group tag and exact match string. For example, this filter value: PU:1000G-mpimg-080821-1_1 would filter out a read with the read group PU:1000G-mpimg-080821-1_1
ReadGroupReadFilter	ReadGroupReadFilter	Keep only reads from the specified read group. Discards reads lacking an RG tag. Matching is done by case-sensitive exact match.
ReadLengthEqualsCigarLengthReadFilter	ReadLengthEqualsCigarLengthReadFilter	Filter out reads where the read and CIGAR do not match in length. Note: unmapped reads pass this filter. See MappedReadFilter for criteria defining an unmapped read.
ReadLengthReadFilter	ReadLengthReadFilter	Keep only reads whose length is ≥ min value and ≤ max value. 
ReadNameReadFilter	ReadNameReadFilter	Keep only reads with this read name. Matching is done by case-sensitive exact match.
ReadStrandFilter	ReadStrandFilter	Keep only reads whose strand is either forward (not 0x10) or reverse (0x10), as specified. By default the filter keeps only forward reads (not 0x10).
SampleReadFilter	SampleReadFilter	Keep only reads for a given sample. Matching is done by case-sensitive exact match.
SecondOfPairReadFilter	SecondOfPairReadFilter	Keep only paired reads (0x1) that are second of pair (0x80). 
SeqIsStoredReadFilter	SeqIsStoredReadFilter	Keep only reads with sequenced bases. 
ValidAlignmentEndReadFilter	ValidAlignmentEndReadFilter	Keep only reads where the read end corresponds to a proper alignment -- that is, the read ends after the start (non-negative number of bases in the reference). 
ValidAlignmentStartReadFilter	ValidAlignmentStartReadFilter	Keep only reads with a valid alignment start (POS larger than 0) or is unmapped. 
WellformedReadFilter	WellformedReadFilter	"Keep only reads that are well-formed. Tests whether a read is ""well-formed"" -- that is, is free of major internal inconsistencies and issues that could lead to errors downstream. If a read passes this filter, the rest of the engine should be able to process it without blowing up. Well-formed reads satisfy 1) Alignment coordinates: start larger than 0 and end after the start position. 2) Alignment agrees with header: contig exists and start is within its range. 3) Read Group and Sequence are present. 4) Consistent read length: bases match in length with the qualities and the CIGAR string. Do not contain skipped regions: represented by the 'N' operator in the CIGAR string."
