Keep only reads that are well-formed
Category Read Filters
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.
Additional references
See these additional references.
- ValidAlignmentStartReadFilter
- ValidAlignmentEndReadFilter
- AlignmentAgreesWithHeaderReadFilter
- HasReadGroupReadFilter
- MatchingBasesAndQualsReadFilter
- ReadLengthEqualsCigarLengthReadFilter
- SeqIsStoredReadFilter
- CigarContainsNoNOperator
GATK version 4.0.4.0 built at 02-47-2019 02:47:54.
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