Generic consensus construction from VCF calls
Version 1

Download RO Crate Run on usegalaxy.eu
Workflow Type: Galaxy

Generic 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

SEEK ID: https://workflowhub.eu/workflows/356?version=1

Inputs

ID Name Description Type
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. n/a
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. n/a
Variant calls Variant calls Collection of VCFs produced by upstream workflows for variation analysis n/a
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. n/a
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. n/a
Reference genome Reference genome The reference genome n/a

Steps

ID Name Description
0 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.
1 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.
2 Variant calls Collection of VCFs produced by upstream workflows for variation analysis
3 min-AF for consensus variant Only variant calls with an allele-frequency greater this value will be considered consensus variants.
4 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.
5 Reference genome The reference genome
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
output output n/a
out1 out1 n/a
out1 out1 n/a
out1 out1 n/a
out_file1 out_file1 n/a
output output n/a
output output n/a
output output n/a
output output n/a
out_file1 out_file1 n/a
out_file1 out_file1 n/a
out_file1 out_file1 n/a
out_file1 out_file1 n/a
out_file1 out_file1 n/a
out_file1 out_file1 n/a
output output n/a
output output n/a
output output n/a
out_file1 out_file1 n/a
out_file1 out_file1 n/a
output_file output_file n/a
output output n/a

Version History

Version 1 (earliest) Created 3rd Jun 2022 at 10:33 by Anton Nekrutenko

Initial commit


Open master ff03aaa
help Creators and Submitter
Creators
Not specified
Additional credit

Wolfgang Maier

Submitter
License
Creative Commons Attribution 4.0
Activity

Views: 400

Created: 3rd Jun 2022 at 10:33

Last used: 7th Oct 2022 at 11:11

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