Package org.broadinstitute.hellbender.engine.filters
package org.broadinstitute.hellbender.engine.filters
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ClassDescriptionFilter out reads where the alignment does not match the contents of the header.Filters out reads that have greater than the threshold number for unknown (N) bases.Wrapper/adapter for
ReadFilterthat counts the number of reads filtered, and provides a filter count summary.Private class for Counting AND filtersWrapper/adapter forVariantFilterthat counts the number of variants filtered, and provides a filter count summary.Private class for Counting AND filtersFilter out reads where the number of soft-/hard-clipped bases on either end is above a certain threshold.Keep only read pairs (0x1) with absolute insert length less than or equal to the specified maximum, and/or greater than or equal to the specified minimum.A simple read filter that allows for the user to specify intervals at the filtering stage.Keep only reads that the attributes of meet a given set of jexl expressionsKeep only reads from the specified library.Keep only reads with mapping qualities within a specified range.Keep only paired reads that are not near each other in a coordinate-sorted source of reads.Filter out reads that: Fail platform/vendor quality checks (0x200) Are unmapped (0x4) Represent secondary/supplementary alignments (0x100 or 0x800)Filters out reads marked as duplicates.Filter out reads where the number of bases without soft-clips (M, I, X, and = CIGAR operators) is lower than a threshold.Keep only reads where the the Read Group platform attribute (RG:PL tag) contains the given string.Filter out reads where the the platform unit attribute (PU tag) contains the given string.Filters which operate onGATKReadshould subclass this by overridingReadFilter.test(GATKRead)ReadFilter implements Predicate and Serializable.Standard ReadFiltersDo not filter out any read.Filter out reads containing skipped region from the reference (CIGAR strings with 'N' operator).Keep only reads that are first of pair (0x1 and 0x40).Keep only reads containing good CIGAR strings.Filter out reads without the SAM record RG (Read Group) tag.Filter out unmapped reads.Filter out reads without available mapping quality (MAPQ=255).Filter out reads with mapping quality equal to zero.Filter out reads where the bases and qualities do not match in length.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.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).Filter reads whose mate is unmapped as well as unmapped reads.If original alignment and mate original alignment tags exist, filter reads that were originally chimeric (mates were on different contigs).Filter out reads with fragment length (insert size) different from zero.Filter out reads that do not align to the reference.Filter out reads marked as duplicate (0x400).Keep only paired reads that are marked as not properly paired (0x1 and !0x2).Filter out reads representing secondary alignments (0x100).Filter out reads representing supplementary alignments (0x800).Filter out unpaired reads (not 0x1).Filter out reads failing platform/vendor quality checks (0x200).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).Keep only paired reads that are properly paired (0x1 and 0x2).Filter out reads where the read and CIGAR do not match in length.Keep only paired reads (0x1) that are second of pair (0x80).Keep only reads with sequenced bases.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).Keep only reads with a valid alignment start (POS larger than 0) or is unmapped.Keep records that don't match the specified filter string(s).Keep only reads from the specified read group.Keep only reads whose length is ≥ min value and ≤ max value.Keep only reads with this read name.Keep only reads whose strand is either forward (not 0x10) or reverse (0x10), as specified.Keep only reads that contain a tag with a value that agrees with parameters as specified.Keep only reads for a given sample.Filter out reads where the ratio of soft-clipped bases to total bases exceeds some given value.Collects common variant filters.Do not filter out any variants.Filter out any variants that are symbolic or SV.Filter out any variants that fail (variant-level) filters.Keep only variants with any of these IDs.Keep only variants with any of these variant types.Tests whether a read is "well-formed" -- that is, is free of major internal inconsistencies and issues that could lead to errors downstream.