--broken <Boolean> |
These are reads where one of the reads in a pair could not be aligned within the required distance or with the correct orientation (default: true) |
-d, --destination <ClcServerObjectUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
-i, --input <ClcObjectUrl> |
Input data on server |
--in-interval <Boolean> |
Only include reads that start and end inside the intervals, excluding reads that only overlap with the intervals (default: true) |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--non-perfect <Boolean> |
These are reads whose alignment can include gaps and mismatches (default: true) |
--non-specific <Boolean> |
These are reads that have multiple possible alignments that are equally good (default: true) |
--non-spliced <Boolean> |
These are reads that are not across an intron (default: true) |
--output-mode <[TRACK, LIST]> |
Choose to output either one Reads Track or one or more Sequence Lists (one for each read group) (default: TRACK) |
--paired <Boolean> |
These are reads where both reads from a pair could be aligned within the required distance and with the correct orientation (default: true) |
--perfect <Boolean> |
These are reads that align perfectly with no gaps or mismatches (default: true) |
--single <Boolean> |
Include reads that were aligned without paired information (default: true) |
--specific <Boolean> |
These are reads that have a single unique best alignment (default: true) |
--spliced <Boolean> |
These are reads that are across an intron (default: true) |
--tracks <ClcObjectUrl> |
Keep reads that overlap with any of these annotation tracks |
