Generic consensus construction from VCF calls Version 1
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Run on usegalaxy.euGeneric consensus building
This workflow generates consensus sequences using a list of variants generated by Variant Calling Workflow.
The workflow accepts a single input:
- A collection of VCF files
The workflow produces a single output:
- Consensus sequence for each input VCF file
The workflow can be accessed at usegalaxy.org
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Depth-threshold for masking | Depth-threshold for masking | Sites in the viral genome covered by less than this number of reads are considered questionable and will be masked (with Ns) in the consensus sequence independent of whether a variant has been called at them or not. |
|
| Reference genome | Reference genome | The reference genome |
|
| Variant calls | Variant calls | Collection of VCFs produced by upstream workflows for variation analysis |
|
| aligned reads data for depth calculation | aligned reads data for depth calculation | Fully processed BAMs as generated by upstream workflows for variation analysis. Note: for ARTIC data, these BAMs should NOT have undergone processing with ivar removereads. |
|
| min-AF for consensus variant | min-AF for consensus variant | Only variant calls with an allele-frequency greater this value will be considered consensus variants. |
|
| min-AF for failed variants | min-AF for failed variants | Variant calls with an allele frequency higher than this value, but lower than the AF threshold for consensus variants will be considered questionable and the respective sites be masked (with Ns) in the consensus sequence. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 6 | bedtools Genome Coverage | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.29.2 |
| 7 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 8 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 9 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 10 | Filter | Filter1 |
| 11 | SnpSift Filter | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1 |
| 12 | SnpSift Filter | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1 |
| 13 | SnpSift Extract Fields | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0 |
| 14 | SnpSift Extract Fields | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0 |
| 15 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6 |
| 16 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6 |
| 17 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6 |
| 18 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6 |
| 19 | Cut | Cut1 |
| 20 | Cut | Cut1 |
| 21 | Concatenate | toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1 |
| 22 | Merge | toolshed.g2.bx.psu.edu/repos/devteam/merge/gops_merge_1/1.0.0 |
| 23 | Subtract | toolshed.g2.bx.psu.edu/repos/devteam/subtract/gops_subtract_1/1.0.0 |
| 24 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6 |
| 25 | Cut | Cut1 |
| 26 | bcftools consensus | toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1 |
| 27 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| coverage_depth | coverage_depth | n/a |
|
| low_cov_regions | low_cov_regions | n/a |
|
| consensus_variants | consensus_variants | n/a |
|
| filter_failed_variants | filter_failed_variants | n/a |
|
| chrom_pos_ref_called_variants | chrom_pos_ref_called_variants | n/a |
|
| chrom_pos_ref_failed_variants | chrom_pos_ref_failed_variants | n/a |
|
| chrom_pos_ref_called_variants_with_0_based_start | chrom_pos_ref_called_variants_with_0_based_start | n/a |
|
| chrom_pos_ref_failed_variants_with_0_based_start | chrom_pos_ref_failed_variants_with_0_based_start | n/a |
|
| chrom_pos_ref_called_variants_with_0_based_start_end | chrom_pos_ref_called_variants_with_0_based_start_end | n/a |
|
| chrom_pos_ref_failed_variants_with_0_based_start_end | chrom_pos_ref_failed_variants_with_0_based_start_end | n/a |
|
| called_variant_sites | called_variant_sites | n/a |
|
| failed_variant_sites | failed_variant_sites | n/a |
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| low_cov_regions_plus_filter_failed | low_cov_regions_plus_filter_failed | n/a |
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| low_cov_regions_plus_filter_failed_combined | low_cov_regions_plus_filter_failed_combined | n/a |
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| masking_regions | masking_regions | n/a |
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| masking_regions_with_1_based_start | masking_regions_with_1_based_start | n/a |
|
| 1_based_masking_regions | 1_based_masking_regions | n/a |
|
| consensus | consensus | n/a |
|
| multisample_consensus_fasta | multisample_consensus_fasta | n/a |
|
Version History
Version 1 (earliest) Created 3rd Jun 2022 at 10:33 by Anton Nekrutenko
Initial commit
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Created: 3rd Jun 2022 at 10:33
AttributionsNone
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https://orcid.org/0000-0002-5987-8032
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