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== Soft Clipping Notes (--clip/-c) ==
== Soft Clipping Notes (--clip/-c) ==
(Version 1.0.14 and later)
When soft clipping:
When soft clipping:
:* if the entire read would be soft clipped, no clipping is done, and instead the read is marked as unmapped
:* if the entire read would be soft clipped, no clipping is done, and instead the read is marked as unmapped
# Run samtools fixmate and pipe it into samtools sort by position
# Run samtools fixmate and pipe it into samtools sort by position
#* <pre> samtools fixmate tempQuerySort.bam - | samtools sort - finalResult</pre>
#* <pre> samtools fixmate tempQuerySort.bam - | samtools sort - finalResult</pre>
= Parameters =
= Parameters =
