Workflow Type: Galaxy

COVID-19: variation analysis reporting

This workflow takes table of variants produced by any of the other four variant calling workflows in and generates a list of variants by Samples and by Variant.


ID Name Description Type
AF Filter AF Filter Allele Frequency Filter. This is the minimum allele frequency required for variants to be included in the report.
  • float?
DP Filter DP Filter Depth Filter. This is the minimum depth of all alignments at a variant site.
  • int?
DP_ALT Filter DP_ALT Filter Depth Filter for variant allele. This is the minimum depth of alignments supporting a variant.
  • int?
Number of Clusters Number of Clusters Number of Clusters to find in Variant Frequency Plot.
  • int?
Variation data to report Variation data to report Variation data in VCF format. Can be the output of any of the workflows in
  • File[]
gene products translations 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
  • File


ID Name Description
6 Compose text parameter value
7 Compose text parameter value
8 SnpSift Filter
9 SnpSift Extract Fields
10 Replace column
11 Datamash
12 Replace
13 Replace
14 Collapse Collection
15 Compute
16 Compute
17 Replace
18 Filter Filter1
19 Datamash
20 Datamash
21 Datamash
22 Datamash
23 Join
24 Join
25 Join
26 Datamash
27 Cut Cut1
28 Join
29 Cut Cut1
30 Split file
31 Cut Cut1
32 Replace
33 Variant Frequency Plot
34 Sort
35 Sort


ID Name Description Type
filtered_variants filtered_variants n/a
  • File
filtered_extracted_variants filtered_extracted_variants n/a
  • File
filtered_and_renamed_effects filtered_and_renamed_effects n/a
  • File
collapsed_effects collapsed_effects n/a
  • File
highest_impact_effects highest_impact_effects n/a
  • File
processed_variants_collection processed_variants_collection n/a
  • File
variants_for_plotting variants_for_plotting n/a
  • File
variant_frequency_plot variant_frequency_plot n/a
  • File
combined_variant_report combined_variant_report n/a
  • File
by_variant_report by_variant_report n/a
  • File

Version History

Version 2 (latest) Created 30th Aug 2021 at 17:01 by Simone Leo

No revision comments

Version 1 (earliest) Created 30th Aug 2021 at 17:00 by Simone Leo

No revision comments

help Creators and Submitter
Not specified
Additional credit

Wolfgang Maier


Views: 1342   Downloads: 232

Created: 30th Aug 2021 at 17:00

Last updated: 30th Aug 2021 at 17:01

help Attributions


Powered by
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH