Workflow: Apply filters to VCF file

Fetched 2021-01-09 04:19:48 GMT
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Inputs

ID Type Title Doc
filter_somatic_llr_normal_contamination_rate Float
known_variants File (Optional)

Previously discovered variants to be flagged in this workflow's output vcf

filter_somatic_llr_tumor_purity Float
filter_mapq0_threshold Float
tumor_sample_name String
tumor_bam File
reference File
filter_minimum_depth Integer
gnomad_field_name String
vcf File
normal_sample_name String
filter_somatic_llr_threshold Float
do_cle_vcf_filter Boolean
filter_gnomADe_maximum_population_allele_frequency Float

Steps

ID Runs Label Doc
filter_vcf_somatic_llr
../tools/filter_vcf_somatic_llr.cwl (CommandLineTool)
use the binomial/llr somatic filter to weed out low confidence variants
filter_vcf_depth
../tools/filter_vcf_depth.cwl (CommandLineTool)
filter variants at sites below a given sequence depth in each sample
filter_known_variants
../tools/filter_known_variants.cwl (CommandLineTool)
Adds an INFO tag (PREVIOUSLY_DISCOVERED) flagging variants in the target vcf present in a known-variants file
filter_vcf_gnomADe_allele_freq
../tools/filter_vcf_custom_allele_freq.cwl (CommandLineTool)
Custom allele frequency filter
filter_vcf_cle
../tools/filter_vcf_cle.cwl (CommandLineTool)
cle_annotated_vcf_filter
set_final_vcf_name
../tools/staged_rename.cwl (CommandLineTool)
Staged Renamer

Renames a file by staging and then `mv`ing it. A workaround for workflow engines that don't support rename.cwl. If running in cwltool, use the other one instead.

filter_vcf_mapq0
../tools/filter_vcf_mapq0.cwl (CommandLineTool)
filter vcf for variants with high percentage of mapq0 reads

Outputs

ID Type Label Doc
filtered_vcf File
Permalink: https://w3id.org/cwl/view/git/b9e7392e72506cadd898a6ac4db330baf6535ab6/definitions/subworkflows/filter_vcf.cwl