Workflow: exome alignment and germline variant detection

Fetched 2023-01-03 20:03:15 GMT
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Inputs

ID Type Title Doc
bam File
intervals 02613b965a63534ce02f028f59f91944[]
reference String
vep_plugins String[] (Optional)
gvcf_gq_bands String[]
synonyms_file File (Optional)
vep_cache_dir String
final_tsv_prefix String (Optional)
custom_gnomad_vcf File (Optional)
custom_clinvar_vcf File (Optional)
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)
vep_ensembl_assembly String

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

contamination_fraction String (Optional)
limit_variant_intervals File
variants_to_table_fields String[] (Optional)
emit_reference_confidence String
variants_to_table_genotype_fields String[] (Optional)

Steps

ID Runs Label Doc
genotype_gvcfs
../tools/gatk_genotypegvcfs.cwl (CommandLineTool)
GATK HaplotypeCaller
limit_variants
../tools/select_variants.cwl (CommandLineTool)
SelectVariants (GATK 3.6)
bgzip_coding_vcf
../tools/bgzip.cwl (CommandLineTool)
bgzip VCF
haplotype_caller scatter GATK HaplotypeCaller over intervals
index_coding_vcf
../tools/index_vcf.cwl (CommandLineTool)
vcf index
annotate_variants
../tools/vep.cwl (CommandLineTool)
Ensembl Variant Effect Predictor
variants_to_table
../tools/variants_to_table.cwl (CommandLineTool)
SelectVariants (GATK 3.6)
bgzip_annotated_vcf
../tools/bgzip.cwl (CommandLineTool)
bgzip VCF
index_annotated_vcf
../tools/index_vcf.cwl (CommandLineTool)
vcf index
coding_variant_filter
../tools/filter_vcf_coding_variant.cwl (CommandLineTool)
Coding Variant filter
add_vep_fields_to_table
../tools/add_vep_fields_to_table.cwl (CommandLineTool)
add VEP annotation to report

Outputs

ID Type Label Doc
gvcf File[]
final_tsv File
final_vcf File
coding_vcf File
limited_vcf File
vep_summary File
Permalink: https://w3id.org/cwl/view/git/18600518ce6539a2e29c1707392a4c5da5687fa3/definitions/subworkflows/germline_detect_variants.cwl