Workflow: exome alignment and germline variant detection

Fetched 2023-01-05 01:21:22 GMT
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Inputs

ID Type Title Doc
cram File
intervals b9e2d1a5d58d24aa094bd25a1be68ba3[]
reference String
coding_only Boolean (Optional)
gvcf_gq_bands String[]
synonyms_file File (Optional)
vep_cache_dir String
custom_gnomad_vcf File (Optional)
custom_clinvar_vcf File (Optional)
contamination_fraction String (Optional)
limit_variant_intervals File
emit_reference_confidence String

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
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

Outputs

ID Type Label Doc
gvcf File[]
final_vcf File
coding_vcf File
limited_vcf File
vep_summary File
Permalink: https://w3id.org/cwl/view/git/5a4fed24f01f6d7c7ce1f595b272d82d97d4f9bd/definitions/subworkflows/germline_detect_variants.cwl