Workflow: Low vaf Detect Variants workflow for Megan Cooper
Fetched 2025-04-27 06:14:22 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bam | File | ||
| docm_vcf | File |
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) |
|
| vep_pick | |||
| reference | File | ||
| sample_name | String | ||
| vep_plugins | String[] | ||
| roi_intervals | File | 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 |
| synonyms_file | File (Optional) | ||
| vep_cache_dir | Directory | ||
| varscan_p_value | Float | ||
| varscan_min_reads | Integer (Optional) | ||
| vep_ensembl_species | String |
ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus |
|
| vep_ensembl_version | String |
ensembl version - Must be present in the cache directory. Example: 95 |
|
| vep_to_table_fields | String[] | ||
| annotate_coding_only | Boolean | ||
| mutect_scatter_count | Integer | ||
| varscan_min_coverage | Integer (Optional) | ||
| varscan_min_var_freq | Float | ||
| vep_ensembl_assembly | String |
genome assembly to use in vep. Examples: GRCh38 or GRCm38 |
|
| varscan_strand_filter | Integer (Optional) | ||
| vep_custom_annotations | https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[] |
custom type, check types directory for input format |
|
| variants_to_table_fields | String[] | ||
| readcount_minimum_base_quality | Integer (Optional) | ||
| readcount_minimum_mapping_quality | Integer (Optional) | ||
| variants_to_table_genotype_fields | String[] | ||
| maximum_population_allele_frequency | Float (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| docm |
../subworkflows/docm_germline.cwl
(Workflow)
|
Detect DoCM variants | |
| index |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| mutect |
../subworkflows/mutect.cwl
(Workflow)
|
mutect parallel workflow | |
| varscan |
../subworkflows/varscan_germline.cwl
(Workflow)
|
Varscan Workflow | |
| af_filter |
../tools/filter_vcf_custom_allele_freq.cwl
(CommandLineTool)
|
Custom allele frequency filter | |
| decompose |
../tools/vt_decompose.cwl
(CommandLineTool)
|
run vt decompose | |
| hard_filter |
../tools/select_variants.cwl
(CommandLineTool)
|
SelectVariants (GATK 4.1.8.1) | |
| bam_readcount |
../tools/bam_readcount.cwl
(CommandLineTool)
|
run bam-readcount | |
| bgzip_filtered |
../tools/bgzip.cwl
(CommandLineTool)
|
bgzip VCF | |
| index_filtered |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| combine_variants |
../tools/general_combine_variants.cwl
(CommandLineTool)
|
CombineVariants (GATK 3.6) | |
| annotate_variants |
../tools/vep.cwl
(CommandLineTool)
|
Ensembl Variant Effect Predictor | |
| variants_to_table |
../tools/variants_to_table.cwl
(CommandLineTool)
|
SelectVariants (GATK 4.1.8.1) | |
| coding_variant_filter |
../tools/filter_vcf_coding_variant.cwl
(CommandLineTool)
|
Coding Variant filter | |
| add_vep_fields_to_table |
../tools/add_vep_fields_to_table.cwl
(CommandLineTool)
|
add VEP annotation to report | |
| add_bam_readcount_to_vcf |
../subworkflows/vcf_readcount_annotator.cwl
(Workflow)
|
Add snv and indel bam-readcount files to a vcf |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| final_tsv | File | ||
| final_vcf | File | ||
| mutect_vcf | File | ||
| varscan_vcf | File | ||
| vep_summary | File | ||
| annotated_vcf | File | ||
| docm_gatk_vcf | File | ||
| tumor_snv_bam_readcount_tsv | File | ||
| tumor_indel_bam_readcount_tsv | File |
Permalink:
https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/pipelines/low_vaf_detect_variants.cwl
