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pipelines_detect_variants.cwl
Travis CI User edited this page Feb 9, 2021
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Detect Variants workflow
Name | Label | Description | Type | Secondary Files |
---|---|---|---|---|
reference | ['string', 'File'] | ['.fai', '^.dict'] | ||
tumor_bam | File | ['.bai', '^.bai'] | ||
normal_bam | File | ['.bai', '^.bai'] | ||
roi_intervals | roi_intervals: regions of interest in which variants will be called | roi_intervals is a list of regions (in interval_list format) within which to call somatic variants | File | |
strelka_exome_mode | boolean | |||
strelka_cpu_reserved | int? | |||
readcount_minimum_base_quality | int? | |||
readcount_minimum_mapping_quality | 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_insert_size | int | |||
docm_vcf | Common mutations in cancer that will be genotyped and passed through into the merged VCF if they have even low-level evidence of a mutation (by default, marked with filter DOCM_ONLY) | File | ['.tbi'] | |
filter_docm_variants | Determines whether variants found only via genotyping of DOCM sites will be filtered (as DOCM_ONLY) or passed through as variant calls | boolean | ||
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']}] | |||
vep_plugins | string[] | |||
filter_gnomADe_maximum_population_allele_frequency | float | |||
filter_mapq0_threshold | float | |||
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 | ||
filter_minimum_depth | int | |||
cle_vcf_filter | boolean | |||
variants_to_table_fields | string[] | |||
variants_to_table_genotype_fields | string[] | |||
vep_to_table_fields | string[] | |||
tumor_sample_name | string | |||
normal_sample_name | string | |||
vep_custom_annotations | custom type, check types directory for input format | ../types/vep_custom_annotation.yml#vep_custom_annotation[] | ||
validated_variants | An optional VCF with variants that will be flagged as 'VALIDATED' if found in this pipeline's main output VCF | File? | ['.tbi'] |
Name | Label | Description | Type | Secondary Files |
---|---|---|---|---|
mutect_unfiltered_vcf | File | ['.tbi'] | ||
mutect_filtered_vcf | File | ['.tbi'] | ||
strelka_unfiltered_vcf | File | ['.tbi'] | ||
strelka_filtered_vcf | File | ['.tbi'] | ||
varscan_unfiltered_vcf | File | ['.tbi'] | ||
varscan_filtered_vcf | File | ['.tbi'] | ||
pindel_unfiltered_vcf | File | ['.tbi'] | ||
pindel_filtered_vcf | File | ['.tbi'] | ||
docm_filtered_vcf | File | ['.tbi'] | ||
final_vcf | File | ['.tbi'] | ||
final_filtered_vcf | File | ['.tbi'] | ||
final_tsv | File | |||
vep_summary | File | |||
tumor_snv_bam_readcount_tsv | File | |||
tumor_indel_bam_readcount_tsv | File | |||
normal_snv_bam_readcount_tsv | File | |||
normal_indel_bam_readcount_tsv | File |
Name | CWL Run |
---|---|
mutect | subworkflows/mutect.cwl |
strelka | subworkflows/strelka_and_post_processing.cwl |
varscan | subworkflows/varscan_pre_and_post_processing.cwl |
pindel | subworkflows/pindel.cwl |
docm | subworkflows/docm_cle.cwl |
combine | tools/combine_variants.cwl |
add_docm_variants | tools/docm_add_variants.cwl |
decompose | tools/vt_decompose.cwl |
decompose_index | tools/index_vcf.cwl |
annotate_variants | tools/vep.cwl |
tumor_bam_readcount | tools/bam_readcount.cwl |
normal_bam_readcount | tools/bam_readcount.cwl |
add_tumor_bam_readcount_to_vcf | subworkflows/vcf_readcount_annotator.cwl |
add_normal_bam_readcount_to_vcf | subworkflows/vcf_readcount_annotator.cwl |
index | tools/index_vcf.cwl |
filter_vcf | subworkflows/filter_vcf.cwl |
annotated_filter_bgzip | tools/bgzip.cwl |
annotated_filter_index | tools/index_vcf.cwl |
variants_to_table | tools/variants_to_table.cwl |
add_vep_fields_to_table | tools/add_vep_fields_to_table.cwl |