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, 14:51, 12 March 2015
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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 |
− | * if the entire read would be soft clipped, no clipping is done, and instead the read is marked as unmapped
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| = Parameters = | | = Parameters = |