Keep only reads where the read end is properly aligned
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 23-40-2018 11:40:56.