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 built at Sat, 23 Nov 2019 16:20:54 -0500.