ValidAlignmentEndReadFilter

Keep only reads where the read end is properly aligned

Category Read Filters

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Overview

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).

This is calculated as:

end - start + 1 ≥ 0
where
start = 1-based inclusive leftmost position of the clipped sequence (0 if no position)
end = 1-based inclusive rightmost position of the clipped sequence (0 if unmapped)


Note: keep also unmapped reads (align to zero bases in the reference). See MappedReadFilter for criteria defining an unmapped read.

Additional references

See these additional references.

• MappedReadFilter

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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.