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 18.104.22.168 built at Wed, 30 Jan 2019 10:21:04 +0530.