Workflow: exome alignment and germline variant detection

Fetched 2023-10-03 09:57:58 GMT
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Inputs

ID Type Title Doc
mills File
omni_vcf File
sequence https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/types/sequence_data.yml#sequence_data[]
dbsnp_vcf File
intervals be6a7138400b68c4f658cfafe80fbd99[]
reference File
vep_plugins String[] (Optional)

array of plugins to use when running vep

known_indels File
gvcf_gq_bands String[]
synonyms_file File (Optional)
vep_cache_dir String
bait_intervals File
bqsr_intervals String[] (Optional)
target_intervals File
summary_intervals https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/types/labelled_file.yml#labelled_file[]
per_base_intervals https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/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

vep_to_table_fields String[] (Optional)
annotate_coding_only Boolean (Optional)
per_target_intervals https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/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/233f026ffce240071edda526391be0c03186fce8/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[]

custom type, check types directory for input format

qc_minimum_base_quality Integer (Optional)
variants_to_table_fields String[] (Optional)
emit_reference_confidence
qc_minimum_mapping_quality Integer (Optional)
picard_metric_accumulation_level String
variants_to_table_genotype_fields String[] (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 exome alignment and germline variant detection
extract_freemix
germline_exome.cwl#extract_freemix/96e11d8b-59d1-485c-9c6c-ec0c3c74c88b (ExpressionTool)
alignment_and_qc
alignment_exome.cwl (Workflow)
exome alignment with qc

Outputs

ID Type Label Doc
cram File
gvcf File[]
final_tsv File
final_vcf File
flagstats File
hs_metrics File
vep_summary File
filtered_tsv File
filtered_vcf File
summary_hs_metrics File[]
insert_size_metrics File
per_base_hs_metrics File[]
verify_bam_id_depth File
insert_size_histogram File
per_target_hs_metrics File[]
verify_bam_id_metrics File
mark_duplicates_metrics File
alignment_summary_metrics File
per_base_coverage_metrics File[]
per_target_coverage_metrics File[]
Permalink: https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/pipelines/germline_exome.cwl