Keep only reads that are well-formed

Category Read Filters

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Overview

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 definition

• Alignment coordinates: start larger than 0 and end after the start position.
• Alignment agrees with header: contig exists and start is within its range.
• Read Group and Sequence are present
• 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.

@see ReadFilterLibrary.ValidAlignmentStartReadFilter @see ReadFilterLibrary.ValidAlignmentEndReadFilter @see AlignmentAgreesWithHeaderReadFilter @see ReadFilterLibrary.HasReadGroupReadFilter @see ReadFilterLibrary.MatchingBasesAndQualsReadFilter @see ReadFilterLibrary.ReadLengthEqualsCigarLengthReadFilter @see ReadFilterLibrary.SeqIsStoredReadFilter @see ReadFilterLibrary.CigarContainsNoNOperator

Additional references

See these additional references.

• ValidAlignmentStartReadFilter
• ValidAlignmentEndReadFilter
• AlignmentAgreesWithHeaderReadFilter
• HasReadGroupReadFilter
• MatchingBasesAndQualsReadFilter
• ReadLengthEqualsCigarLengthReadFilter
• SeqIsStoredReadFilter
• CigarContainsNoNOperator

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GATK version 4.5.0.0 built at Tue, 9 Jan 2024 14:37:17 -0500.