Workflow: Apply filters to VCF file
Fetched 2023-01-11 04:33:49 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| vcf | File | ||
| reference | File | ||
| tumor_bam | File | ||
| do_cle_vcf_filter | Boolean | ||
| gnomad_field_name | String | ||
| tumor_sample_name | String | ||
| normal_sample_name | String | ||
| validated_variants | File (Optional) |
An optional VCF with variants that will be flagged as 'VALIDATED' if found in this pipeline's main output VCF |
|
| filter_minimum_depth | Integer | ||
| filter_mapq0_threshold | Float | ||
| filter_somatic_llr_threshold | Float | ||
| filter_somatic_llr_tumor_purity | Float | ||
| filter_somatic_llr_normal_contamination_rate | Float | ||
| filter_gnomADe_maximum_population_allele_frequency | Float |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| filter_vcf_cle |
../tools/filter_vcf_cle.cwl
(CommandLineTool)
|
cle_annotated_vcf_filter | |
| filter_vcf_depth |
../tools/filter_vcf_depth.cwl
(CommandLineTool)
|
filter variants at sites below a given sequence depth in each sample | |
| filter_vcf_mapq0 |
../tools/filter_vcf_mapq0.cwl
(CommandLineTool)
|
filter vcf for variants with high percentage of mapq0 reads | |
| 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_known_variants |
../tools/filter_known_variants.cwl
(CommandLineTool)
|
Adds an INFO tag (VALIDATED) flagging variants in the pipeline vcf present in a previously validated vcf file | |
| 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_gnomADe_allele_freq |
../tools/filter_vcf_custom_allele_freq.cwl
(CommandLineTool)
|
Custom allele frequency filter |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| filtered_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/389f6edccab082d947bee9c032f59dbdf9f7c325/definitions/subworkflows/filter_vcf.cwl
