| 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? |
|
| trimming |
|
|
['../types/trimming_options.yml#trimming_options', 'null'] |
|
| 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[] |
|
| target_intervals |
|
|
File |
|
| per_base_intervals |
|
|
../types/labelled_file.yml#labelled_file[] |
|
| per_target_intervals |
|
|
../types/labelled_file.yml#labelled_file[] |
|
| qc_intervals |
|
|
File |
|
| summary_intervals |
|
|
../types/labelled_file.yml#labelled_file[] |
|
| omni_vcf |
|
|
File |
['.tbi'] |
| picard_metric_accumulation_level |
|
|
string |
|
| qc_minimum_mapping_quality |
|
|
int? |
|
| qc_minimum_base_quality |
|
|
int? |
|
| strelka_cpu_reserved |
|
|
int? |
|
| scatter_count |
|
scatters each supported variant detector (varscan, mutect) into this many parallel jobs |
int |
|
| mutect_artifact_detection_mode |
|
|
boolean |
|
| mutect_max_alt_allele_in_normal_fraction |
|
|
float? |
|
| mutect_max_alt_alleles_in_normal_count |
|
|
int? |
|
| varscan_strand_filter |
|
|
int? |
|
| varscan_min_coverage |
|
|
int? |
|
| varscan_min_var_freq |
|
|
float? |
|
| varscan_p_value |
|
|
float? |
|
| varscan_max_normal_freq |
|
|
float? |
|
| docm_vcf |
|
|
File |
['.tbi'] |
| filter_docm_variants |
|
|
boolean? |
|
| filter_somatic_llr_threshold |
|
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. |
float |
|
| filter_somatic_llr_tumor_purity |
|
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 |
float |
|
| filter_somatic_llr_normal_contamination_rate |
|
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 |
float |
|
| 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? |
|
| 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[] |
|
| manta_call_regions |
|
|
File? |
['.tbi'] |
| manta_non_wgs |
|
|
boolean? |
|
| manta_output_contigs |
|
|
boolean? |
|
| somalier_vcf |
|
|
File |
|
| tumor_sample_name |
|
|
string |
|
| normal_sample_name |
|
|
string |
|
| validated_variants |
|
An optional VCF with variants that will be flagged as 'VALIDATED' if found in this pipeline's main output VCF |
File? |
['.tbi'] |
| cnvkit_target_average_size |
|
approximate size of split target bins for CNVkit; if not set a suitable window size will be set by CNVkit automatically |
int? |
|