vcf2lineage 1.0
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Associated Tutorial
This workflows is part of the tutorial Automating Galaxy workflows using the command line, available in the GTN
Thanks to...
Workflow Author(s): Wolfgang Maier
Tutorial Author(s): Simon Bray, Wolfgang Maier
Tutorial Contributor(s): Helena Rasche, Saskia Hiltemann, Wolfgang Maier, Bérénice Batut, Martin Čech, Björn Grüning, Armin Dadras
Funder(s): ELIXIR Europe, de.NBI, University of Freiburg
Grants(s): EuroScienceGateway
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Reference genome | #main/Reference genome | n/a |
|
| Variant calls | #main/Variant calls | n/a |
|
| min-AF for consensus variant | #main/min-AF for consensus variant | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 4 | SnpSift Filter | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1 |
| 5 | bcftools consensus | toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10 |
| 6 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 |
| 7 | Pangolin | toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| consensus | #main/consensus | n/a |
|
| consensus_variants | #main/consensus_variants | n/a |
|
| multisample_consensus_fasta | #main/multisample_consensus_fasta | n/a |
|
| pangolin_results | #main/pangolin_results | n/a |
|
Version History
master
Creators and Submitter
Views: 1100 Downloads: 163 Runs: 0
Created: 2nd Jun 2025 at 10:51
AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
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