pipelines_tumor_only_detect_variants.cwl - genome/analysis-workflows GitHub Wiki
Documentation for tumor_only_detect_variants.cwl
This page is auto-generated. Do not edit.
Overview
Tumor-Only Detect Variants workflow
Inputs
| Name |
Label |
Description |
Type |
Secondary Files |
| reference |
|
|
['string', 'File'] |
['.fai', '^.dict'] |
| bam |
|
|
File |
['^.bai', '.bai'] |
| roi_intervals |
roi_intervals: regions of interest in which variants will be called |
roi_intervals is a list of regions (in interval_list format) within which to call somatic variants |
File |
|
| varscan_strand_filter |
|
|
int? |
|
| varscan_min_coverage |
|
|
int? |
|
| varscan_min_var_freq |
|
|
float? |
|
| varscan_p_value |
|
|
float? |
|
| varscan_min_reads |
|
|
int? |
|
| maximum_population_allele_frequency |
|
|
float? |
|
| vep_cache_dir |
|
|
['string', 'Directory'] |
|
| vep_ensembl_assembly |
|
genome assembly to use in vep. Examples: GRCh38 or GRCm38 |
string |
|
| vep_ensembl_version |
|
ensembl version - Must be present in the cache directory. Example: 95 |
string |
|
| vep_ensembl_species |
|
ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus |
string |
|
| synonyms_file |
|
|
File? |
|
| annotate_coding_only |
|
|
boolean |
|
| vep_pick |
|
|
['null', {'type': 'enum', 'symbols': ['pick', 'flag_pick', 'pick_allele', 'per_gene', 'pick_allele_gene', 'flag_pick_allele', 'flag_pick_allele_gene']}] |
|
| variants_to_table_fields |
|
|
string[] |
|
| variants_to_table_genotype_fields |
|
|
string[] |
|
| vep_to_table_fields |
|
|
string[] |
|
| vep_plugins |
|
|
string[] |
|
| sample_name |
|
|
string |
|
| docm_vcf |
|
Common mutations in cancer that will be genotyped and passed through into the merged VCF if they have even low-level evidence of a mutation (by default, marked with filter DOCM_ONLY) |
File |
['.tbi'] |
| vep_custom_annotations |
|
custom type, check types directory for input format |
../types/vep_custom_annotation.yml#vep_custom_annotation[] |
|
| readcount_minimum_mapping_quality |
|
|
int? |
|
| readcount_minimum_base_quality |
|
|
int? |
|
Outputs
| Name |
Label |
Description |
Type |
Secondary Files |
| varscan_vcf |
|
|
File |
['.tbi'] |
| docm_gatk_vcf |
|
|
File |
|
| annotated_vcf |
|
|
File |
['.tbi'] |
| final_vcf |
|
|
File |
['.tbi'] |
| final_tsv |
|
|
File |
|
| vep_summary |
|
|
File |
|
| tumor_snv_bam_readcount_tsv |
|
|
File |
|
| tumor_indel_bam_readcount_tsv |
|
|
File |
|
Steps