subworkflows_germline_filter_vcf.cwl
Travis CI User edited this page Feb 24, 2021
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Apply filters to VCF file
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| annotated_vcf | File | |||
| filter_gnomAD_maximum_population_allele_frequency | float | |||
| gnomad_field_name | string | |||
| limit_variant_intervals | File | |||
| reference | ['string', 'File'] | ['.fai', '^.dict'] |
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| filtered_vcf | File | ['.tbi'] | ||
| final_vcf | File | ['.tbi'] |
| Name | CWL Run |
|---|---|
| coding_variant_filter | tools/filter_vcf_coding_variant.cwl |
| gnomad_frequency_filter | tools/filter_vcf_custom_allele_freq.cwl |
| set_filtered_vcf_name | tools/staged_rename.cwl |
| bgzip_filtered_vcf | tools/bgzip.cwl |
| index_filtered_vcf | tools/index_vcf.cwl |
| limit_variants | tools/select_variants.cwl |