Workflow: gathered exome alignment and somatic variant detection for cle purpose
Fetched 2024-05-12 21:07:32 GMT
Verified with cwltool version 3.1.20230201224320
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- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| 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) |
|
| omni_vcf | File | ||
| vep_pick | |||
| reference | String | ||
| output_dir | String | ||
| tumor_name | String (Optional) | ||
| normal_name | String (Optional) | ||
| somalier_vcf | File | ||
| scatter_count | Integer |
scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs |
|
| synonyms_file | File (Optional) | ||
| vep_cache_dir | Directory | ||
| bait_intervals | File | ||
| bqsr_intervals | String[] | ||
| cle_vcf_filter | Boolean | ||
| tumor_sequence | https://w3id.org/cwl/view/git/8da2b1cd6fa379b2c22baf9dad762d39630e6f46/definitions/types/sequence_data.yml#sequence_data[] | tumor_sequence: MT sequencing data and readgroup information |
tumor_sequence represents the sequencing data for the MT sample as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required. |
| disclaimer_text | String (Optional) | ||
| normal_sequence | https://w3id.org/cwl/view/git/8da2b1cd6fa379b2c22baf9dad762d39630e6f46/definitions/types/sequence_data.yml#sequence_data[] | normal_sequence: WT sequencing data and readgroup information |
normal_sequence represents the sequencing data for the WT sample as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required. |
| varscan_p_value | Float (Optional) | ||
| bqsr_known_sites | File[] |
One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis. |
|
| target_intervals | File | target_intervals: interval_list file of targets used in the sequencing experiment |
target_intervals is an interval_list corresponding to the targets for the capture reagent. Bed files with this information can be converted to interval_lists with Picard BedToIntervalList. In general for a WES exome reagent bait_intervals and target_intervals are the same. |
| summary_intervals | https://w3id.org/cwl/view/git/8da2b1cd6fa379b2c22baf9dad762d39630e6f46/definitions/types/labelled_file.yml#labelled_file[] | ||
| tumor_sample_name | String | ||
| disclaimer_version | String | ||
| normal_sample_name | String | ||
| per_base_intervals | https://w3id.org/cwl/view/git/8da2b1cd6fa379b2c22baf9dad762d39630e6f46/definitions/types/labelled_file.yml#labelled_file[] | ||
| pindel_insert_size | Integer | ||
| 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 (Optional) | ||
| filter_docm_variants | Boolean (Optional) |
Determines whether variants found only via genotyping of DOCM sites will be filtered (as DOCM_ONLY) or passed through as variant calls |
|
| filter_minimum_depth | Integer (Optional) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/8da2b1cd6fa379b2c22baf9dad762d39630e6f46/definitions/types/labelled_file.yml#labelled_file[] | ||
| strelka_cpu_reserved | Integer (Optional) | ||
| varscan_min_coverage | Integer (Optional) | ||
| varscan_min_var_freq | Float (Optional) | ||
| 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/8da2b1cd6fa379b2c22baf9dad762d39630e6f46/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[] |
custom type, check types directory for input format |
|
| qc_minimum_base_quality | Integer (Optional) | ||
| target_interval_padding | Integer | target_interval_padding |
The effective coverage of capture products generally extends out beyond the actual regions targeted. This parameter allows variants to be called in these wingspan regions, extending this many base pairs from each side of the target regions. |
| varscan_max_normal_freq | Float (Optional) | ||
| variants_to_table_fields | String[] | ||
| qc_minimum_mapping_quality | Integer (Optional) | ||
| filter_somatic_llr_threshold | Float |
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. |
|
| filter_somatic_llr_tumor_purity | Float |
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 |
|
| picard_metric_accumulation_level | String | ||
| variants_to_table_genotype_fields | String[] | ||
| filter_somatic_llr_normal_contamination_rate | Float |
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 |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gatherer |
../tools/gatherer.cwl
(CommandLineTool)
|
||
| somatic_exome |
somatic_exome_cle.cwl
(Workflow)
|
exome alignment and somatic variant detection for cle purpose |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| final_outputs | String[] |
https://w3id.org/cwl/view/git/8da2b1cd6fa379b2c22baf9dad762d39630e6f46/definitions/pipelines/somatic_exome_cle_gathered.cwl
