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26 bytes added
, 23:28, 12 November 2017
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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 |
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| # 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> |
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| = Parameters = | | = Parameters = |