Workflow: Vcf concordance evaluation workflow
Fetched 2023-01-11 20:12:22 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- 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 |
|---|---|---|---|
| roi_bed | File | ||
| base_vcf | File | ||
| query_vcf | File | ||
| reference | File | ||
| output_dir | String | ||
| base_tumor_cram | File | ||
| base_normal_cram | File | ||
| query_tumor_cram | File | ||
| query_normal_cram | File | ||
| tumor_sample_name | String (Optional) | ||
| normal_sample_name | String (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sompy |
../tools/sompy.cwl
(CommandLineTool)
|
som.py compares variants in vcf by location and alleles (using bcftools isec). | |
| vaf_report |
../tools/eval_vaf_report.cwl
(CommandLineTool)
|
Generate vaf report for concordance analysis | |
| combine_vcf |
../tools/combine_variants_concordance.cwl
(CommandLineTool)
|
CombineVariants (GATK 3.6) | |
| plot_output |
../tools/somatic_concordance_graph.cwl
(CommandLineTool)
|
Generate somatic concordance report graph | |
| base_vcf_pass |
../tools/select_variants.cwl
(CommandLineTool)
|
SelectVariants (GATK 3.6) | |
| query_vcf_pass |
../tools/select_variants.cwl
(CommandLineTool)
|
SelectVariants (GATK 3.6) | |
| base_vcf_pass_roi |
../tools/bedtools_intersect.cwl
(CommandLineTool)
|
||
| query_vcf_pass_roi |
../tools/bedtools_intersect.cwl
(CommandLineTool)
|
||
| gather_to_sub_directory |
../tools/gather_to_sub_directory.cwl
(CommandLineTool)
|
||
| base_tumor_bam_readcount |
../tools/bam_readcount.cwl
(CommandLineTool)
|
run bam-readcount | |
| base_normal_bam_readcount |
../tools/bam_readcount.cwl
(CommandLineTool)
|
run bam-readcount | |
| query_tumor_bam_readcount |
../tools/bam_readcount.cwl
(CommandLineTool)
|
run bam-readcount | |
| query_normal_bam_readcount |
../tools/bam_readcount.cwl
(CommandLineTool)
|
run bam-readcount | |
| bgzip_and_index_base_pass_roi |
bgzip_and_index.cwl
(Workflow)
|
bgzip and index VCF | |
| bgzip_and_index_query_pass_roi |
bgzip_and_index.cwl
(Workflow)
|
bgzip and index VCF | |
| base_tumor_cram_to_bam_and_index |
cram_to_bam_and_index.cwl
(Workflow)
|
cram_to_bam workflow | |
| base_normal_cram_to_bam_and_index |
cram_to_bam_and_index.cwl
(Workflow)
|
cram_to_bam workflow | |
| query_tumor_cram_to_bam_and_index |
cram_to_bam_and_index.cwl
(Workflow)
|
cram_to_bam workflow | |
| query_normal_cram_to_bam_and_index |
cram_to_bam_and_index.cwl
(Workflow)
|
cram_to_bam workflow |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_directory | Directory |
Permalink:
https://w3id.org/cwl/view/git/ac87e0584685fe04e4010ecd77ae4f055f21d788/definitions/subworkflows/vcf_eval_concordance.cwl
