--breakpoints <Boolean> |
Create breakpoints (default: false) |
--broken-pairs <Boolean> |
When selected, broken pair reads will be ignored. (default: true) |
-d, --destination <ClcServerObjectUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
--filter <Boolean> |
Filter variants (default: false) |
-i, --input <ClcObjectUrl> |
Input data on server |
--indel <Boolean> |
Create InDel variations (default: true) |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--masking-track <ClcObjectUrl> |
Analysis will only be performed in the specified regions |
--max-mismatch |
|
Integer: >= 0 |
When examining positions for excess of unaligned ends, only reads mapped with this or fewer mismatches will be considered. (default: 3) |
--min-consensus-coverage |
|
Double: 0.0 <= x < 1.0 |
Stop unaligned end consensus generation when coverage drops below the specified fraction of the initial coverage (default: 0.0) |
--min-qscore |
|
Byte: 0 <= x <= 64 |
Ignore bases with Q-score below threshold (default: 0) |
--min-reads |
|
Integer: >= 2 |
Mininum number of reads supporting this variant, before the variant will be reported. (default: 2) |
--pvalue |
|
Double: 0.0 < x <= 1.0 |
Threshold for calling significance in the Binomial distribution of unaligned end reads. (default: 1.0E-4) |
--report <Boolean> |
Create Report (default: true) |
--variants <Boolean> |
Create interchromosomal variations (default: true) |
