Generic consensus construction from VCF calls
Version 1

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Run on Galaxy

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
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.	int?
Reference genome	Reference genome	The reference genome	File
Variant calls	Variant calls	Collection of VCFs produced by upstream workflows for variation analysis	File[]
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.	File[]
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.	float?
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.	float?

Steps

ID	Name	Description
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
coverage_depth	coverage_depth	n/a	File
low_cov_regions	low_cov_regions	n/a	File
consensus_variants	consensus_variants	n/a	File
filter_failed_variants	filter_failed_variants	n/a	File
chrom_pos_ref_called_variants	chrom_pos_ref_called_variants	n/a	File
chrom_pos_ref_failed_variants	chrom_pos_ref_failed_variants	n/a	File
chrom_pos_ref_called_variants_with_0_based_start	chrom_pos_ref_called_variants_with_0_based_start	n/a	File
chrom_pos_ref_failed_variants_with_0_based_start	chrom_pos_ref_failed_variants_with_0_based_start	n/a	File
chrom_pos_ref_called_variants_with_0_based_start_end	chrom_pos_ref_called_variants_with_0_based_start_end	n/a	File
chrom_pos_ref_failed_variants_with_0_based_start_end	chrom_pos_ref_failed_variants_with_0_based_start_end	n/a	File
called_variant_sites	called_variant_sites	n/a	File
failed_variant_sites	failed_variant_sites	n/a	File
low_cov_regions_plus_filter_failed	low_cov_regions_plus_filter_failed	n/a	File
low_cov_regions_plus_filter_failed_combined	low_cov_regions_plus_filter_failed_combined	n/a	File
masking_regions	masking_regions	n/a	File
masking_regions_with_1_based_start	masking_regions_with_1_based_start	n/a	File
1_based_masking_regions	1_based_masking_regions	n/a	File
consensus	consensus	n/a	File
multisample_consensus_fasta	multisample_consensus_fasta	n/a	File