Keep only reads where the read end is properly aligned
Category Read Filters
OverviewKeep 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
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.
See these additional references.
GATK version 188.8.131.52-SNAPSHOT built at Mon, 7 Feb 2022 11:18:01 -0500.