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, 18:09, 12 March 2015
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| This parameter was added in version 1.0.10. | | This parameter was added in version 1.0.10. |
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| + | === Mark entirely clipped reads as unmapped (<code>--unmapped</code>)=== |
| + | Specify this option if instead of marking reads as entirely clipped, mark them as unmapped. |
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| + | 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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| {{noeofBGZFParameter}} | | {{noeofBGZFParameter}} |