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→Overview of the clipOverlap function of bamUtil: Fix broken link.
When two mates overlap, this tool will clip the record's whose clipped region would has the lowest average quality.
When two mates overlap, this tool will clip the record's whose clipped region would has the lowest average quality.
It also checks strand. If a forward strand extends past the end of a reverse strand, that will be clipped. Similarly, if a reverse strand starts before the forward strand, the region prior to the forward strand will be clipped. If the reverse strand occurs entirely before the forward strand, both strands will be entirely clipped. If the [[#Mark entirely clipped reads as unmapped (<code>--unmapped</code>)|<code>--unmapped</code>]] option is specified rather than clipping an entire read, it will be marked as unmapped.
It also checks strand. If a forward strand extends past the end of a reverse strand, that will be clipped. Similarly, if a reverse strand starts before the forward strand, the region prior to the forward strand will be clipped. If the reverse strand occurs entirely before the forward strand, both strands will be entirely clipped. If the [[#Mark entirely clipped reads as unmapped (--unmapped)|<code>--unmapped</code>]] option is specified rather than clipping an entire read, it will be marked as unmapped.
The qualities on the two strands remain unchanged even with clipping.
The qualities on the two strands remain unchanged even with clipping.
