pipelines_detect_variants_wgs_nonhuman.cwl - genome/analysis-workflows GitHub Wiki
Documentation for detect_variants_wgs_nonhuman.cwl
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Overview
Detect Variants workflow for nonhuman WGS pipeline
Inputs
| Name |
Label |
Description |
Type |
Secondary Files |
| reference |
|
|
['string', 'File'] |
['.fai', '^.dict'] |
| tumor_bam |
|
|
File |
['.bai', '^.bai'] |
| normal_bam |
|
|
File |
['.bai', '^.bai'] |
| roi_intervals |
|
|
File |
|
| strelka_exome_mode |
|
|
boolean |
|
| strelka_cpu_reserved |
|
|
int? |
|
| readcount_minimum_base_quality |
|
|
int? |
|
| readcount_minimum_mapping_quality |
|
|
int? |
|
| scatter_count |
|
scatters each supported variant detector (varscan, mutect) into this many parallel jobs |
int? |
|
| varscan_strand_filter |
|
|
int? |
|
| varscan_min_coverage |
|
|
int? |
|
| varscan_min_var_freq |
|
|
float? |
|
| varscan_p_value |
|
|
float? |
|
| varscan_max_normal_freq |
|
|
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']}] |
|
| vep_plugins |
|
|
string[]? |
|
| filter_mapq0_threshold |
|
|
float? |
|
| filter_minimum_depth |
|
|
int? |
|
| filter_somatic_llr_threshold |
|
Sets the stringency (log-likelihood ratio) used to filter out non-somatic variants. Typical values are 10=high stringency, 5=normal, 3=low stringency. Low stringency may be desirable when read depths are low (as in WGS) or when tumor samples are impure. |
float |
|
| filter_somatic_llr_tumor_purity |
|
Sets the purity of the tumor used in the somatic llr filter, used to remove non-somatic variants. Probably only needs to be adjusted for low-purity (< 50%). Range is 0 to 1 |
float |
|
| filter_somatic_llr_normal_contamination_rate |
|
Sets the fraction of tumor present in the normal sample (range 0 to 1), used in the somatic llr filter. Useful for heavily contaminated adjacent normals. Range is 0 to 1 |
float |
|
| cle_vcf_filter |
|
|
boolean? |
|
| variants_to_table_fields |
|
|
string[]? |
|
| variants_to_table_genotype_fields |
|
|
string[]? |
|
| vep_to_table_fields |
|
|
string[]? |
|
| tumor_sample_name |
|
|
string |
|
| normal_sample_name |
|
|
string |
|
Outputs
| Name |
Label |
Description |
Type |
Secondary Files |
| mutect_unfiltered_vcf |
|
|
File |
['.tbi'] |
| mutect_filtered_vcf |
|
|
File |
['.tbi'] |
| strelka_unfiltered_vcf |
|
|
File |
['.tbi'] |
| strelka_filtered_vcf |
|
|
File |
['.tbi'] |
| varscan_unfiltered_vcf |
|
|
File |
['.tbi'] |
| varscan_filtered_vcf |
|
|
File |
['.tbi'] |
| final_vcf |
|
|
File |
['.tbi'] |
| final_filtered_vcf |
|
|
File |
['.tbi'] |
| final_tsv |
|
|
File |
|
| vep_summary |
|
|
File |
|
| tumor_snv_bam_readcount_tsv |
|
|
File |
|
| tumor_indel_bam_readcount_tsv |
|
|
File |
|
| normal_snv_bam_readcount_tsv |
|
|
File |
|
| normal_indel_bam_readcount_tsv |
|
|
File |
|
Steps