| reference |
|
|
string |
|
| tumor_sequence |
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. |
../types/sequence_data.yml#sequence_data[] |
|
| tumor_name |
|
|
string? |
|
| normal_sequence |
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. |
../types/sequence_data.yml#sequence_data[] |
|
| normal_name |
|
|
string? |
|
| followup_sequence |
|
|
../types/sequence_data.yml#sequence_data[] |
|
| followup_name |
|
|
string? |
|
| bqsr_known_sites |
|
One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis. |
File[] |
['.tbi'] |
| bqsr_intervals |
|
|
string[] |
|
| bait_intervals |
|
|
File |
|
| target_intervals |
|
|
File |
|
| per_base_intervals |
|
|
../types/labelled_file.yml#labelled_file[] |
|
| per_target_intervals |
|
|
../types/labelled_file.yml#labelled_file[] |
|
| summary_intervals |
|
|
../types/labelled_file.yml#labelled_file[] |
|
| omni_vcf |
|
|
File |
['.tbi'] |
| emit_reference_confidence |
|
|
{'type': 'enum', 'symbols': ['NONE', 'BP_RESOLUTION', 'GVCF']} |
|
| gvcf_gq_bands |
|
|
string[] |
|
| intervals |
|
|
{'type': 'array', 'items': {'type': 'array', 'items': 'string'}} |
|
| variant_reporting_intervals |
|
|
File |
|
| picard_metric_accumulation_level |
|
|
string |
|
| qc_minimum_mapping_quality |
|
|
int? |
|
| qc_minimum_base_quality |
|
|
int? |
|
| interval_list |
|
|
File |
|
| strelka_cpu_reserved |
|
|
int? |
|
| scatter_count |
|
scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs |
int |
|
| varscan_strand_filter |
|
|
int? |
|
| varscan_min_coverage |
|
|
int? |
|
| varscan_min_var_freq |
|
|
float? |
|
| varscan_p_value |
|
|
float? |
|
| varscan_max_normal_freq |
|
|
float? |
|
| pindel_region_file |
|
|
File |
|
| pindel_insert_size |
|
|
int |
|
| docm_vcf |
|
|
File |
['.tbi'] |
| filter_docm_variants |
|
|
boolean? |
|
| filter_minimum_depth |
|
|
int? |
|
| vep_cache_dir |
|
|
['string', 'Directory'] |
|
| vep_ensembl_assembly |
|
genome assembly to use in vep. Examples: GRCh38 or GRCm38 |
string |
|
| vep_ensembl_version |
|
ensembl version - Must be present in the cache directory. Example: 95 |
string |
|
| vep_ensembl_species |
|
ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus |
string |
|
| synonyms_file |
|
|
File? |
|
| annotate_coding_only |
|
|
boolean? |
|
| germline_coding_only |
|
|
boolean? |
|
| vep_pick |
|
|
['null', {'type': 'enum', 'symbols': ['pick', 'flag_pick', 'pick_allele', 'per_gene', 'pick_allele_gene', 'flag_pick_allele', 'flag_pick_allele_gene']}] |
|
| cle_vcf_filter |
|
|
boolean |
|
| variants_to_table_fields |
|
|
string[] |
|
| variants_to_table_genotype_fields |
|
|
string[] |
|
| vep_to_table_fields |
|
|
string[] |
|
| vep_custom_annotations |
|
custom type, check types directory for input format |
../types/vep_custom_annotation.yml#vep_custom_annotation[] |
|
| germline_tsv_prefix |
|
|
string? |
|
| germline_variants_to_table_fields |
|
|
string[] |
|
| germline_variants_to_table_genotype_fields |
|
|
string[] |
|
| germline_vep_to_table_fields |
|
|
string[] |
|
| somalier_vcf |
|
|
File |
|
| output_dir |
|
|
string |
|
| disclaimer_version |
|
|
string |
|
| tumor_sample_name |
|
|
string |
|
| normal_sample_name |
|
|
string |
|
| disclaimer_text |
|
|
string? |
|