--cds-track <ClcObjectUrl> |
Select CDS track |
-d, --destination <ClcServerObjectUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
--downstream-flanking-bases |
|
Integer: 0 <= x <= 100000 |
Include this many 3' flanking positions for c. annotation (default: 2000) |
--filter-empty-cds <Boolean> |
Filter away CDS regions with no overlapping variants (default: true) |
--filter-synonymous <Boolean> |
Filter away synonymous variants (default: false) |
--genetic-code <Genetic code> |
Genetic code used for amino acid translation. (default: 1 Standard) |
-i, --input <ClcObjectUrl> |
Input data on server |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--mrna-prioritized <Boolean> |
Use priorities on transcripts to select which annotations to add (default: false) |
--mrna-track <ClcObjectUrl> |
Select mRNA track |
--output-hgvs-compliant-variant-track <Boolean> |
Move variants with ambiguous positions from their VCF compliant location (left-aligned) to the location reflecting the HGVS standard for annotation (most 3' relative to the transcript orientation). This option does not affect the HGVS annotation that this tool adds to each variant. This option is recommended if variants will be uploaded to Ingenuity Variant Analysis or QCI Interpret. (default: false) |
--sequence-track <ClcObjectUrl> |
Select reference sequence track |
--upstream-flanking-bases |
|
Integer: 0 <= x <= 100000 |
Include this many 5' flanking positions for c. annotation (default: 5000) |
