Keep only reads where the read end is properly aligned
Category Read Filters
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.
GATK version 4.0.5.1 built at 25-59-2019 01:59:53.
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