sars-cov-2-consensus-from-variation/COVID-19-CONSENSUS-CONSTRUCTION
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Run on GalaxyBuild a consensus sequence from FILTER PASS variants with intrasample allele-frequency above a configurable consensus threshold. Hard-mask regions with low coverage (but not consensus variants within them) and ambiguous sites.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Depth-threshold for masking | #main/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 | #main/Reference genome | The SARS-CoV-2 reference genome |
|
| Variant calls | #main/Variant calls | Collection of VCFs produced by upstream workflows for variation analysis |
|
| aligned reads data for depth calculation | #main/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 | #main/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 | #main/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 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 7 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 8 | bedtools Genome Coverage | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0 |
| 9 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 10 | SnpSift Filter | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1 |
| 11 | SnpSift Filter | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1 |
| 12 | Filter | Filter1 |
| 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_column1/2.0 |
| 16 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
| 17 | Concatenate | toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1 |
| 18 | Merge | toolshed.g2.bx.psu.edu/repos/devteam/merge/gops_merge_1/1.0.0 |
| 19 | Subtract | toolshed.g2.bx.psu.edu/repos/devteam/subtract/gops_subtract_1/1.0.0 |
| 20 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
| 21 | bcftools consensus | toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3 |
| 22 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| 1_based_masking_regions | #main/1_based_masking_regions | n/a |
|
| called_variant_sites | #main/called_variant_sites | n/a |
|
| chrom_pos_ref_called_variants | #main/chrom_pos_ref_called_variants | n/a |
|
| chrom_pos_ref_failed_variants | #main/chrom_pos_ref_failed_variants | n/a |
|
| consensus | #main/consensus | n/a |
|
| consensus_af_threshold | #main/consensus_af_threshold | n/a |
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| consensus_variants | #main/consensus_variants | n/a |
|
| coverage_depth | #main/coverage_depth | n/a |
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| depth_threshold | #main/depth_threshold | n/a |
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| failed_variant_sites | #main/failed_variant_sites | n/a |
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| filter_failed_variants | #main/filter_failed_variants | n/a |
|
| low_cov_regions | #main/low_cov_regions | n/a |
|
| low_cov_regions_plus_filter_failed | #main/low_cov_regions_plus_filter_failed | n/a |
|
| low_cov_regions_plus_filter_failed_combined | #main/low_cov_regions_plus_filter_failed_combined | n/a |
|
| masking_regions | #main/masking_regions | n/a |
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| multisample_consensus_fasta | #main/multisample_consensus_fasta | n/a |
|
| non_consensus_af_threshold | #main/non_consensus_af_threshold | n/a |
|
Version History
v0.4.3 (latest) Created 26th Mar 2025 at 12:00 by WorkflowHub Bot
Updated to v0.4.3
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v0.4.34504880
v0.2 (earliest) Created 23rd Jul 2021 at 10:18 by WorkflowHub Bot
Added/updated 10 files
Frozen
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Views: 9802 Downloads: 2019 Runs: 0
Created: 23rd Jul 2021 at 10:18
Last updated: 26th Mar 2025 at 10:06
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Teams: Intergalactic Workflow Commission (IWC), Vertebrate Genomes Pipelines in Galaxy, nf-core
Organizations: Bots, European Galaxy Team
https://orcid.org/0000-0002-9464-6640
IWC - Intergalactic Workflow Commission
Space: This Team is not associated with a Space
Public web page: https://github.com/galaxyproject/iwc
Workflows developed by or used by BY-COVID project.
The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data. Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, ...
