sars-cov-2-variation-reporting/COVID-19-VARIATION-REPORTING
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Run on GalaxyThis workflow takes a VCF dataset of variants produced by any of the *-variant-calling workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates tabular lists of variants by Samples and by Variant, and an overview plot of variants and their allele-frequencies.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| AF Filter | #main/AF Filter | Allele Frequency Filter. This is the minimum allele frequency required for variants to be included in the reports. |
|
| DP Filter | #main/DP Filter | Depth Filter. This is the minimum depth of all alignments at a variant site. |
|
| DP_ALT Filter | #main/DP_ALT Filter | Depth Filter for variant allele. This is the minimum depth of alignments supporting a variant. |
|
| Number of Clusters | #main/Number of Clusters | Number of Clusters to use in Variant Frequency Plot. |
|
| Variation data to report | #main/Variation data to report | Variation data in VCF format. Can be the output of any of the workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling |
|
| gene products translations | #main/gene products translations | A custom tabular file mapping NCBI RefSeq Protein identifiers as used by snpEff version 4.5covid19 to their commonly used names. Can be obtained from https://doi.org/10.5281/zenodo.4555734 |
|
Steps
| ID | Name | Description |
|---|---|---|
| 6 | SnpSift Filter | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1 |
| 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 | SnpSift Filter | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1 |
| 10 | SnpSift Extract Fields | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0 |
| 11 | Replace column | toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2 |
| 12 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1 |
| 13 | Datamash | toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0 |
| 14 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1 |
| 15 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 16 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1 |
| 17 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1 |
| 18 | Datamash | toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0 |
| 19 | Filter | Filter1 |
| 20 | Datamash | toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0 |
| 21 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1 |
| 22 | Datamash | toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0 |
| 23 | Datamash | toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0 |
| 24 | Datamash | toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0 |
| 25 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1 |
| 26 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1 |
| 27 | Cut | Cut1 |
| 28 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1 |
| 29 | Cut | Cut1 |
| 30 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1 |
| 31 | Cut | Cut1 |
| 32 | Split file | toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 |
| 33 | Sort | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1 |
| 34 | Sort | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1 |
| 35 | Variant Frequency Plot | toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| af_filter_threshold | #main/af_filter_threshold | n/a |
|
| af_recalculated | #main/af_recalculated | n/a |
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| all_variants_all_samples | #main/all_variants_all_samples | n/a |
|
| by_variant_report | #main/by_variant_report | n/a |
|
| collapsed_effects | #main/collapsed_effects | n/a |
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| combined_variant_report | #main/combined_variant_report | n/a |
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| dp_alt_filter_threshold | #main/dp_alt_filter_threshold | n/a |
|
| dp_filter_threshold | #main/dp_filter_threshold | n/a |
|
| filtered_and_renamed_effects | #main/filtered_and_renamed_effects | n/a |
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| filtered_extracted_variants | #main/filtered_extracted_variants | n/a |
|
| filtered_variants | #main/filtered_variants | n/a |
|
| highest_impact_effects | #main/highest_impact_effects | n/a |
|
| plot_number_of_clusters | #main/plot_number_of_clusters | n/a |
|
| prefiltered_variants | #main/prefiltered_variants | n/a |
|
| variant_frequency_plot | #main/variant_frequency_plot | n/a |
|
| variants_for_plotting | #main/variants_for_plotting | n/a |
|
Version History
v0.3.4 (latest) Created 7th Oct 2024 at 16:31 by WorkflowHub Bot
Updated to v0.3.4
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v0.3.48f39392
v0.1 (earliest) Created 12th Mar 2021 at 13:41 by WorkflowHub Bot
Added/updated 13 files
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Views: 16397 Downloads: 12308 Runs: 4
Created: 12th Mar 2021 at 13:41
Last updated: 18th Aug 2025 at 18:27
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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, ...
