Workflow: Whole genome alignment and somatic variant detection
Fetched 2024-10-25 06:28:09 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| docm_vcf | File | ||
| omni_vcf | File | ||
| trimming | https://w3id.org/cwl/view/git/9cbf2a483e1b9e4cdb8e2564be27a9e64fc1169e/definitions/types/trimming_options.yml#trimming_options (Optional) | ||
| vep_pick | |||
| reference | String | ||
| tumor_name | String (Optional) | ||
| normal_name | String (Optional) | ||
| qc_intervals | File | ||
| somalier_vcf | File | ||
| manta_non_wgs | Boolean (Optional) | ||
| scatter_count | Integer |
scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs |
|
| synonyms_file | File (Optional) | ||
| vep_cache_dir | Directory | ||
| bqsr_intervals | String[] | ||
| cle_vcf_filter | Boolean | ||
| tumor_sequence | https://w3id.org/cwl/view/git/9cbf2a483e1b9e4cdb8e2564be27a9e64fc1169e/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/9cbf2a483e1b9e4cdb8e2564be27a9e64fc1169e/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 | ||
| summary_intervals | https://w3id.org/cwl/view/git/9cbf2a483e1b9e4cdb8e2564be27a9e64fc1169e/definitions/types/labelled_file.yml#labelled_file[] | ||
| tumor_sample_name | String | ||
| manta_call_regions | File (Optional) | ||
| normal_sample_name | String | ||
| per_base_intervals | https://w3id.org/cwl/view/git/9cbf2a483e1b9e4cdb8e2564be27a9e64fc1169e/definitions/types/labelled_file.yml#labelled_file[] | ||
| pindel_insert_size | Integer | ||
| validated_variants | File (Optional) |
An optional VCF with variants that will be flagged as 'VALIDATED' if found in this pipeline's main output VCF |
|
| 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) | ||
| manta_output_contigs | Boolean (Optional) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/9cbf2a483e1b9e4cdb8e2564be27a9e64fc1169e/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/9cbf2a483e1b9e4cdb8e2564be27a9e64fc1169e/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[] |
custom type, check types directory for input format |
|
| qc_minimum_base_quality | Integer (Optional) | ||
| 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. |
|
| mutect_artifact_detection_mode | Boolean | ||
| 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[] | ||
| mutect_max_alt_alleles_in_normal_count | Integer (Optional) | ||
| mutect_max_alt_allele_in_normal_fraction | Float (Optional) | ||
| 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 |
|---|---|---|---|
| manta |
../tools/manta_somatic.cwl
(CommandLineTool)
|
Set up and execute manta | |
| concordance |
../tools/concordance.cwl
(CommandLineTool)
|
Concordance checking between Tumor and Normal BAM | |
| detect_variants |
detect_variants_wgs.cwl
(Workflow)
|
Detect Variants workflow for WGS pipeline | |
| 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 | |
| tumor_alignment_and_qc |
alignment_wgs.cwl
(Workflow)
|
wgs alignment with qc | |
| normal_alignment_and_qc |
alignment_wgs.cwl
(Workflow)
|
wgs alignment with qc |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| final_tsv | File | ||
| final_vcf | File | ||
| tumor_cram | File | ||
| normal_cram | File | ||
| vep_summary | File | ||
| all_candidates | File | ||
| tumor_flagstats | File | ||
| diploid_variants | File (Optional) | ||
| normal_flagstats | File | ||
| small_candidates | File | ||
| somatic_variants | File (Optional) | ||
| docm_filtered_vcf | File | ||
| tumor_wgs_metrics | File | ||
| final_filtered_vcf | File | ||
| normal_wgs_metrics | File | ||
| mutect_filtered_vcf | File | ||
| tumor_only_variants | File (Optional) | ||
| strelka_filtered_vcf | File | ||
| varscan_filtered_vcf | File | ||
| mutect_unfiltered_vcf | File | ||
| tumor_gc_bias_metrics | File | ||
| normal_gc_bias_metrics | 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[] | ||
| tumor_verify_bam_id_depth | File | ||
| normal_insert_size_metrics | File | ||
| normal_per_base_hs_metrics | File[] | ||
| normal_verify_bam_id_depth | File | ||
| tumor_gc_bias_metrics_chart | File | ||
| tumor_insert_size_histogram | File | ||
| tumor_per_target_hs_metrics | File[] | ||
| tumor_snv_bam_readcount_tsv | File | ||
| tumor_verify_bam_id_metrics | File | ||
| normal_gc_bias_metrics_chart | File | ||
| normal_insert_size_histogram | File | ||
| normal_per_target_hs_metrics | File[] | ||
| normal_snv_bam_readcount_tsv | File | ||
| normal_verify_bam_id_metrics | File | ||
| somalier_concordance_metrics | File | ||
| tumor_gc_bias_metrics_summary | File | ||
| tumor_indel_bam_readcount_tsv | File | ||
| tumor_mark_duplicates_metrics | File | ||
| normal_gc_bias_metrics_summary | File | ||
| normal_indel_bam_readcount_tsv | File | ||
| normal_mark_duplicates_metrics | File | ||
| somalier_concordance_statistics | 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/9cbf2a483e1b9e4cdb8e2564be27a9e64fc1169e/definitions/pipelines/somatic_wgs.cwl
