Workflow: exome alignment and tumor-only variant detection
Fetched 2023-01-04 16:49:06 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| docm_vcf | File | ||
| omni_vcf | File | ||
| sequence | https://w3id.org/cwl/view/git/97572e3a088d79f6a4166385f79e79ea77b11470/definitions/types/sequence_data.yml#sequence_data[] | sequence: sequencing data and readgroup information |
sequence represents the sequencing data as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required. |
| trimming | https://w3id.org/cwl/view/git/97572e3a088d79f6a4166385f79e79ea77b11470/definitions/types/trimming_options.yml#trimming_options (Optional) | ||
| vep_pick | |||
| reference | File | ||
| sample_name | String | ||
| synonyms_file | File (Optional) | ||
| vep_cache_dir | Directory | ||
| bait_intervals | File | ||
| bqsr_intervals | String[] (Optional) | ||
| 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/97572e3a088d79f6a4166385f79e79ea77b11470/definitions/types/labelled_file.yml#labelled_file[] | ||
| varscan_min_reads | Integer (Optional) | ||
| per_base_intervals | https://w3id.org/cwl/view/git/97572e3a088d79f6a4166385f79e79ea77b11470/definitions/types/labelled_file.yml#labelled_file[] | ||
| 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[] (Optional) | ||
| annotate_coding_only | Boolean (Optional) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/97572e3a088d79f6a4166385f79e79ea77b11470/definitions/types/labelled_file.yml#labelled_file[] | ||
| 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/97572e3a088d79f6a4166385f79e79ea77b11470/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: number of bp flanking each target region in which to allow variant calls |
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. |
| variants_to_table_fields | String[] (Optional) | ||
| qc_minimum_mapping_quality | Integer (Optional) | ||
| readcount_minimum_base_quality | Integer (Optional) | ||
| picard_metric_accumulation_level | String | ||
| readcount_minimum_mapping_quality | Integer (Optional) | ||
| variants_to_table_genotype_fields | String[] (Optional) | ||
| maximum_population_allele_frequency | Float (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| index_cram |
../tools/index_cram.cwl
(CommandLineTool)
|
samtools index cram | |
| bam_to_cram |
../tools/bam_to_cram.cwl
(CommandLineTool)
|
BAM to CRAM conversion | |
| detect_variants |
tumor_only_detect_variants.cwl
(Workflow)
|
Tumor-Only Detect Variants workflow | |
| alignment_and_qc |
alignment_exome.cwl
(Workflow)
|
exome alignment with qc | |
| pad_target_intervals |
../tools/interval_list_expand.cwl
(CommandLineTool)
|
expand interval list regions by a given number of basepairs |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| cram | File | ||
| final_tsv | File | ||
| final_vcf | File | ||
| flagstats | File | ||
| hs_metrics | File | ||
| varscan_vcf | File | ||
| vep_summary | File | ||
| annotated_vcf | File | ||
| docm_gatk_vcf | File | ||
| summary_hs_metrics | File[] | ||
| insert_size_metrics | File | ||
| per_base_hs_metrics | File[] | ||
| verify_bam_id_depth | File | ||
| insert_size_histogram | File | ||
| per_target_hs_metrics | File[] | ||
| verify_bam_id_metrics | File | ||
| mark_duplicates_metrics | File | ||
| alignment_summary_metrics | File | ||
| per_base_coverage_metrics | File[] | ||
| per_target_coverage_metrics | File[] | ||
| tumor_snv_bam_readcount_tsv | File | ||
| tumor_indel_bam_readcount_tsv | File |
https://w3id.org/cwl/view/git/97572e3a088d79f6a4166385f79e79ea77b11470/definitions/pipelines/tumor_only_exome.cwl
