Workflow: wgs alignment and tumor-only variant detection

Fetched 2023-01-04 21:09:11 GMT
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Inputs

ID Type Title Doc
mills File
docm_vcf File
omni_vcf File
sequence https://w3id.org/cwl/view/git/74647cc0f1abac4ee22950cfa89c44cf2ca3cffd/definitions/types/sequence_data.yml#sequence_data[]
vep_pick
dbsnp_vcf File
reference File
sample_name String
known_indels File
qc_intervals File
synonyms_file File (Optional)
vep_cache_dir Directory
summary_intervals https://w3id.org/cwl/view/git/74647cc0f1abac4ee22950cfa89c44cf2ca3cffd/definitions/types/labelled_file.yml#labelled_file[]
per_base_intervals https://w3id.org/cwl/view/git/74647cc0f1abac4ee22950cfa89c44cf2ca3cffd/definitions/types/labelled_file.yml#labelled_file[]
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

per_target_intervals https://w3id.org/cwl/view/git/74647cc0f1abac4ee22950cfa89c44cf2ca3cffd/definitions/types/labelled_file.yml#labelled_file[]
vep_ensembl_assembly String

genome assembly to use in vep. Examples: GRCh38 or GRCm38

vep_custom_annotations https://w3id.org/cwl/view/git/74647cc0f1abac4ee22950cfa89c44cf2ca3cffd/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[]

custom type, check types directory for input format

variant_detection_intervals File
readcount_minimum_base_quality Integer (Optional)
picard_metric_accumulation_level String
readcount_minimum_mapping_quality Integer (Optional)

Steps

ID Runs Label Doc
index_cram
../tools/index_cram.cwl (CommandLineTool)
samtools index cram
bam_to_cram
../tools/bam_to_cram.cwl (CommandLineTool)
BAM to CRAM conversion
detect_variants Tumor-Only Detect Variants workflow
alignment_and_qc
alignment_wgs.cwl (Workflow)
wgs alignment with qc

Outputs

ID Type Label Doc
cram File
final_tsv File
final_vcf File
flagstats File
varscan_vcf File
vep_summary File
wgs_metrics File
annotated_vcf File
docm_gatk_vcf File
gc_bias_metrics File
summary_hs_metrics File[]
insert_size_metrics File
per_base_hs_metrics File[]
verify_bam_id_depth File
gc_bias_metrics_chart File
insert_size_histogram File
per_target_hs_metrics File[]
verify_bam_id_metrics File
gc_bias_metrics_summary File
mark_duplicates_metrics File
alignment_summary_metrics File
per_base_coverage_metrics File[]
per_target_coverage_metrics File[]
tumor_snv_bam_readcount_tsv File
tumor_indel_bam_readcount_tsv File
Permalink: https://w3id.org/cwl/view/git/74647cc0f1abac4ee22950cfa89c44cf2ca3cffd/definitions/pipelines/tumor_only_wgs.cwl