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
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 these additional references.
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GATK version 184.108.40.206 built at Wed, 30 Jan 2019 10:21:04 +0530.