Workflow Type: Galaxy
Open
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
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
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master
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Wolfgang Maier
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Views: 117
Created: 3rd Jun 2022 at 10:33
Last used: 29th Jun 2022 at 04:05
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