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 4.1.8.1-SNAPSHOT built at Sun, 2 Aug 2020 22:56:07 -0400.
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