subworkflows_varscan.cwl - genome/analysis-workflows GitHub Wiki
Documentation for varscan.cwl
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Overview
varscan somatic workflow
Inputs
| Name |
Label |
Description |
Type |
Secondary Files |
| reference |
|
|
['string', 'File'] |
['.fai', '^.dict'] |
| tumor_bam |
|
|
File |
['^.bai'] |
| normal_bam |
|
|
File |
['^.bai'] |
| roi_bed |
|
|
File? |
|
| strand_filter |
|
|
int? |
|
| min_coverage |
|
|
int? |
|
| min_var_freq |
|
|
float? |
|
| p_value |
|
|
float? |
|
| max_normal_freq |
|
|
float? |
|
Outputs
| Name |
Label |
Description |
Type |
Secondary Files |
| snvs |
|
|
File |
|
| indels |
|
|
File |
|
| somatic_hc_snvs |
|
|
File |
|
| somatic_snvs |
|
|
File |
|
| germline_hc_snvs |
|
|
File |
|
| germline_snvs |
|
|
File |
|
| loh_hc_snvs |
|
|
File |
|
| loh_snvs |
|
|
File |
|
| somatic_hc_indels |
|
|
File |
|
| somatic_indels |
|
|
File |
|
| germline_hc_indels |
|
|
File |
|
| germline_indels |
|
|
File |
|
| loh_hc_indels |
|
|
File |
|
| loh_indels |
|
|
File |
|
Steps