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Keep only reads that are well-formed

Category Read Filters


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.

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GATK version built at Wed, 9 Oct 2019 15:19:59 -0400.