subworkflows_germline_detect_variants.cwl - genome/analysis-workflows GitHub Wiki
Documentation for germline_detect_variants.cwl
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Overview
exome alignment and germline variant detection
Inputs
| Name |
Label |
Description |
Type |
Secondary Files |
| reference |
|
|
['string', 'File'] |
['.fai', '^.dict'] |
| bam |
|
|
File |
['^.bai'] |
| gvcf_gq_bands |
|
|
string[] |
|
| intervals |
|
|
{'type': 'array', 'items': {'type': 'array', 'items': 'string'}} |
|
| contamination_fraction |
|
|
string? |
|
| ploidy |
|
|
int? |
|
| 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 |
|
| vep_plugins |
|
|
string[] |
|
| synonyms_file |
|
|
File? |
|
| annotate_coding_only |
|
|
boolean? |
|
| vep_custom_annotations |
|
custom type, check types directory for input format |
../types/vep_custom_annotation.yml#vep_custom_annotation[] |
|
| limit_variant_intervals |
|
|
File |
|
| variants_to_table_fields |
|
|
string[]? |
|
| variants_to_table_genotype_fields |
|
|
string[]? |
|
| vep_to_table_fields |
|
|
string[]? |
|
| final_tsv_prefix |
|
|
string? |
|
| filter_gnomAD_maximum_population_allele_frequency |
|
|
float |
|
Outputs
| Name |
Label |
Description |
Type |
Secondary Files |
| raw_vcf |
|
|
File |
['.tbi'] |
| final_vcf |
|
|
File |
['.tbi'] |
| filtered_vcf |
|
|
File |
['.tbi'] |
| vep_summary |
|
|
File |
|
| final_tsv |
|
|
File |
|
| filtered_tsv |
|
|
File |
|
Steps