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When soft clipping (--clip/-c):
When soft clipping (--clip/-c):
* output is not sorted (start positions may change after soft clipping)
* if the entire read would be soft clipped, no clipping is done, and instead the read is marked as unmapped
* mate information is not updated (start positions/mapping may change after soft clipping)
** run samtools fixmate to fix mate information (will first need to sort by read name)
* output is not sorted (start positions/mapping may change after soft clipping)
** run samtools sort to resort by coordinate (after fixmate)
* soft clips already in the read are maintained or added to
* soft clips already in the read are maintained or added to
** if 3 bases were clipped and 2 are specified to be clipped, no change is made to that end
** if 3 bases were clipped and 2 are specified to be clipped, no change is made to that end
** if 3 bases were clipped and 5 are specified to be clipped, 2 additional bases are clipped from that end
** if 3 bases were clipped and 5 are specified to be clipped, 2 additional bases are clipped from that end
= Parameters =
= Parameters =
