aliquot-maf-cwl

CWL tools and workflows for generating and processing aliquot-MAF

Convert annotated VCF to an aliquot MAF

Workflow: workflows/vcf_to_aliquot_maf_wf.cwl

Inputs

Input	Type	Description
annotated_vcf_uuid	uuid	input vcf uuid
annotated_vcf_index_uuid	uuid	input vcf index uuid
bioclient_config	file	bioclient config file
biotype_priority_uuid	uuid	biotype priority json uuid
caller_id	string	variant caller id
case_uuid	uuid	case uuid
context_size	int	reference context size (5)
cosmic_vcf_uuid	uuid	cosmic vcf uuid
cosmic_vcf_index_uuid	uuid	cosmic vcf index uuid
custom_enst_uuid	uuid	custom transcript overloads file uuid
dbsnp_priority_db_uuid	uuid	dbSNP priority sqlite uuid
effect_priority_uuid	uuid	effect prioty json uuid
exac_freq_cutoff	float	non-tcga exac frequency filter cutoff (0.001)
experimental_strategy	string	experimental strategy
gdc_blacklist_uuid	uuid	blacklist uuid if doing blacklist filter
gdc_pon_vcf_uuid	uuid	panel of normals vcf uuid
gdc_pon_vcf_index_uuid	uuid	panel of normals vcf index uuid
hotspot_tsv_uuid	uuid	hotspot tsv uuid
job_uuid	uuid	uuid of the workflow job
maf_center	string[]	list of sequencing centers
min_n_depth	int	normal depth filtering cutoff (7)
non_tcga_exac_vcf_uuid	uuid	Non-TCGA ExAC vcf uuid
non_tcga_exac_vcf_index_uuid	uuid	Non-TCGA ExAC vcf index uuid
nonexonic_intervals_uuid	uuid	Exonic regions bed uuid
nonexonic_intervals_index_uuid	uuid	Exonic regions bed tabix index uuid
normal_aliquot_uuid	uuid	normal aliquot uuid
normal_bam_uuid	uuid	normal sample's bam uuid
normal_submitter_id	string	normal aliquot's submitted id
reference_fasta_index_uuid	uuid	main chromosome reference fai uuid
reference_fasta_uuid	uuid	main chromosome reference fasta uuid
sequencer	string[]	list of sequencers used
target_intervals_record	indexed_file[]	list of targeted sequencing indexed_file objects
tumor_aliquot_uuid	uuid	tumor aliquot uuid
tumor_bam_uuid	uuid	tumor aliquot's bam uuid
tumor_submitter_id	string	tumor aliquot's submitter id
upload_bucket	string	upload bucket uri

An indexed_file object id defined as:

{
  "main_file_uuid": "<UUID>",
  "index_file_uuid": "<UUID>"
}

Outputs

• aliquot_maf_uuid - the UUID of the generated aliquot MAF file

Aggregate/merge aliquot MAF from different callers

Workflow: workflows/ensemble_aliquot_maf_wf.cwl

Inputs

Input	Type	Description
aliquot_maf_uuid_list	optional_file_uuid[]	input list of optional_file_uuid objects
bioclient_config	file	bioclient config file
experimental_strategy	string	experimental strategy
job_uuid	uuid	uuid of the workflow job
min_callers	int	minimum number of callers supporting the variant for masked merged maf file (2)
min_n_depth	float	minimal Normal depth cutoff after averaging (7)
upload_bucket	string	upload bucket uri

An optional_file_uuid object:

{
    "key": "<caller>",
    "uuid": "<maf_uuid>"
}

Outputs

• aliquot_merged_raw_maf_uuid - the UUID of the raw merged MAF
• aliquot_merged_masked_maf_uuid - the UUID of the masked merged MAF
• aliquot_maf_metrics_uuid - the UUID of the metrics JSON file