-d, --destination <ClcServerObjectUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
--force-guiding-variants <Boolean> |
Forces reads to be realigned to guidance-variants. Use with (intrinsic) variants called on the data set to be realigned. Do NOT use with (extrinsic) variants, such as dbSNP / Cosmic annotations. (default: false) |
--guidance-variant-track <ClcObjectUrl> |
Track of variants used to guide the realignment. |
-i, --input <ClcObjectUrl> |
Input data on server |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--max-extrinsic-variant-length |
|
Integer: 1 <= x <= 100000 |
Guidance variants longer than threshold length will be ignored (default: 200) |
--output-mode <[TRACK, CLUSTER]> |
Whether to output a read-mapping-track or a legacy read-mapping. (default: CLUSTER) |
--output-roi-track <Boolean> |
Output a track of regions-of-interest informing about where realignment has improved the data set. (default: true) |
--realign-unaligned-ends <Boolean> |
Attempt to align any unaligned read ends, also known as soft-clipped read ends, in the mapping. (default: true) |
--realignment-passes |
|
Integer: 1 <= x <= 10 |
How many iterations should the realigner perform. (default: 2) |
