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This parameter was added in version 1.0.10.
This parameter was added in version 1.0.10.
=== Mark entirely clipped reads as unmapped (<code>--unmapped</code>)===
Specify this option if instead of marking reads as entirely clipped, mark them as unmapped.
When marking a read as unmapped, it will:
* Set CIGAR to 0
* Set MapQ to 0
* Clear N/A flag fields:
** Proper pair
** Secondary Alignment
** Supplementary Alignment
* Update the Mate's flag to indicate:
** Mate Unmapped
** Not proper pair
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