Workflow: exome alignment and germline variant detection

Fetched 2021-06-16 23:43:30 GMT
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Inputs

ID Type Title Doc
reference String
emit_reference_confidence String
contamination_fraction String (Optional)
intervals f27d1ed5affb64066822476de0d768bf[]
vep_cache_dir String (Optional)
cram File
limit_variant_intervals File
synonyms_file File (Optional)
gvcf_gq_bands String[]
hgvs_annotation Boolean (Optional)
coding_only Boolean (Optional)
custom_gnomad_vcf File (Optional)

Steps

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

Outputs

ID Type Label Doc
coding_vcf File
final_vcf File
gvcf File[]
vep_summary File
limited_vcf File
Permalink: https://w3id.org/cwl/view/git/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/detect_variants/germline_detect_variants.cwl