Workflow: exome alignment and somatic variant detection
Fetched 2023-01-03 20:57:21 GMT
Verified with cwltool version 3.1.20221201130942
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- Default Values
- Nested Workflows
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- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| trimming | https://w3id.org/cwl/view/git/174f3b239018328cec1d821947438b457552724c/definitions/types/trimming_options.yml#trimming_options (Optional) | ||
| vep_pick | |||
| reference | File | ||
| tumor_name | String (Optional) | tumor_name: String specifying the name of the MT sample |
tumor_name provides a string for what the MT sample will be referred to in the various outputs, for example the VCF files. |
| normal_name | String (Optional) | normal_name: String specifying the name of the WT sample |
normal_name provides a string for what the WT sample will be referred to in the various outputs, for example the VCF files. |
| 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 | ||
| cle_vcf_filter | Boolean | ||
| tumor_sequence | https://w3id.org/cwl/view/git/174f3b239018328cec1d821947438b457552724c/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. |
| normal_sequence | https://w3id.org/cwl/view/git/174f3b239018328cec1d821947438b457552724c/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) | ||
| 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/174f3b239018328cec1d821947438b457552724c/definitions/types/labelled_file.yml#labelled_file[] | ||
| tumor_sample_name | String | ||
| normal_sample_name | String | ||
| per_base_intervals | https://w3id.org/cwl/view/git/174f3b239018328cec1d821947438b457552724c/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) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/174f3b239018328cec1d821947438b457552724c/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) | ||
| 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. |
| 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 |
|---|---|---|---|
| detect_variants |
detect_variants_nonhuman.cwl
(Workflow)
|
Detect Variants workflow | |
| tumor_index_cram |
../tools/index_cram.cwl
(CommandLineTool)
|
samtools index cram | |
| normal_index_cram |
../tools/index_cram.cwl
(CommandLineTool)
|
samtools index cram | |
| tumor_bam_to_cram |
../tools/bam_to_cram.cwl
(CommandLineTool)
|
BAM to CRAM conversion | |
| normal_bam_to_cram |
../tools/bam_to_cram.cwl
(CommandLineTool)
|
BAM to CRAM conversion | |
| pad_target_intervals |
../tools/interval_list_expand.cwl
(CommandLineTool)
|
expand interval list regions by a given number of basepairs | |
| tumor_alignment_and_qc |
alignment_exome_nonhuman.cwl
(Workflow)
|
exome alignment with qc, no bqsr, no verify_bam_id | |
| normal_alignment_and_qc |
alignment_exome_nonhuman.cwl
(Workflow)
|
exome alignment with qc, no bqsr, no verify_bam_id |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| final_tsv | File | ||
| final_vcf | File | ||
| tumor_cram | File | ||
| normal_cram | File | ||
| vep_summary | File | ||
| tumor_flagstats | File | ||
| normal_flagstats | File | ||
| tumor_hs_metrics | File | ||
| normal_hs_metrics | File | ||
| final_filtered_vcf | File | ||
| mutect_filtered_vcf | File | ||
| pindel_filtered_vcf | File | ||
| strelka_filtered_vcf | File | ||
| varscan_filtered_vcf | File | ||
| mutect_unfiltered_vcf | File | ||
| pindel_unfiltered_vcf | File | ||
| strelka_unfiltered_vcf | File | ||
| varscan_unfiltered_vcf | File | ||
| tumor_summary_hs_metrics | File[] | ||
| normal_summary_hs_metrics | File[] | ||
| tumor_insert_size_metrics | File | ||
| tumor_per_base_hs_metrics | File[] | ||
| normal_insert_size_metrics | File | ||
| normal_per_base_hs_metrics | File[] | ||
| tumor_per_target_hs_metrics | File[] | ||
| tumor_snv_bam_readcount_tsv | File | ||
| normal_per_target_hs_metrics | File[] | ||
| normal_snv_bam_readcount_tsv | File | ||
| tumor_indel_bam_readcount_tsv | File | ||
| tumor_mark_duplicates_metrics | File | ||
| normal_indel_bam_readcount_tsv | File | ||
| normal_mark_duplicates_metrics | File | ||
| tumor_alignment_summary_metrics | File | ||
| tumor_per_base_coverage_metrics | File[] | ||
| normal_alignment_summary_metrics | File | ||
| normal_per_base_coverage_metrics | File[] | ||
| tumor_per_target_coverage_metrics | File[] | ||
| normal_per_target_coverage_metrics | File[] |
https://w3id.org/cwl/view/git/174f3b239018328cec1d821947438b457552724c/definitions/pipelines/somatic_exome_nonhuman.cwl
