Workflow: exome alignment and variant detection

Fetched 2019-11-20 21:54:27 GMT
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Inputs

ID Type Title Doc
picard_metric_accumulation_level String
qc_minimum_mapping_quality Integer (Optional)
per_base_intervals File
bams File[]
target_intervals File
reference String
qc_minimum_base_quality Integer (Optional)
varscan_strand_filter Integer (Optional)
varscan_p_value Float (Optional)
readgroups String[]
variants_to_table_fields String[] (Optional)
annotate_coding_only Boolean (Optional)
varscan_min_var_freq Float (Optional)
variants_to_table_genotype_fields String[] (Optional)
vep_to_table_fields String[] (Optional)
sample_name String
custom_gnomad_vcf File (Optional)
omni_vcf File
vep_cache_dir String (Optional)
varscan_min_coverage Integer (Optional)
bqsr_intervals String[] (Optional)
readcount_minimum_mapping_quality Integer (Optional)
mills File
docm_vcf File
readcount_minimum_base_quality Integer (Optional)
maximum_population_allele_frequency Float (Optional)
hgvs_annotation Boolean (Optional)
known_indels File
per_target_intervals File
bait_intervals File
varscan_min_reads Integer (Optional)
per_base_bait_intervals File
dbsnp_vcf File
synonyms_file File (Optional)
per_target_bait_intervals File

Steps

ID Runs Label Doc
alignment_and_qc
exome_alignment.cwl (Workflow)
exome alignment with qc
detect_variants Tumor-Only Detect Variants workflow

Outputs

ID Type Label Doc
per_target_coverage_metrics File (Optional)
final_vcf File
vep_summary File
mark_duplicates_metrics File
insert_size_metrics File
per_base_hs_metrics File (Optional)
insert_size_histogram File
verify_bam_id_depth File
hs_metrics File
annotated_vcf File
cram File
varscan_vcf File
alignment_summary_metrics File
verify_bam_id_metrics File
tumor_bam_readcount_tsv File
per_target_hs_metrics File (Optional)
final_tsv File
docm_gatk_vcf File
flagstats File
per_base_coverage_metrics File (Optional)
Permalink: https://w3id.org/cwl/view/git/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/exome_workflow.cwl