sars-cov-2-consensus-from-variation/COVID-19-CONSENSUS-CONSTRUCTION
v0.4.3 (latest)

v0.4.3 (latest)

v0.4.2

v0.4.1

v0.1

v0.4

v0.3

v0.2.2

v0.2.1

v0.2 (earliest)

Workflow Type: Galaxy

Build a consensus sequence from FILTER PASS variants with intrasample allele-frequency above a configurable consensus threshold. Hard-mask regions with low coverage (but not consensus variants within them) and ambiguous sites.

SEEK ID: https://workflowhub.eu/workflows/138?version=9

Inputs

ID	Name	Description	Type
Depth-threshold for masking	#main/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	#main/Reference genome	The SARS-CoV-2 reference genome	File
Variant calls	#main/Variant calls	Collection of VCFs produced by upstream workflows for variation analysis	array containing File
aligned reads data for depth calculation	#main/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.	array containing File
min-AF for consensus variant	#main/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	#main/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	Compose text parameter value	toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
7	Compose text parameter value	toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
8	bedtools Genome Coverage	toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1
9	Compose text parameter value	toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
10	SnpSift Filter	toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1
11	SnpSift Filter	toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1
12	Filter	Filter1
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_column1/2.1
16	Compute	toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
17	Concatenate	toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1
18	Merge	toolshed.g2.bx.psu.edu/repos/devteam/merge/gops_merge_1/1.0.0
19	Subtract	toolshed.g2.bx.psu.edu/repos/devteam/subtract/gops_subtract_1/1.0.0
20	Compute	toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
21	bcftools consensus	toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4
22	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0

Outputs

ID	Name	Description	Type
1_based_masking_regions	#main/1_based_masking_regions	n/a	File
called_variant_sites	#main/called_variant_sites	n/a	File
chrom_pos_ref_called_variants	#main/chrom_pos_ref_called_variants	n/a	File
chrom_pos_ref_failed_variants	#main/chrom_pos_ref_failed_variants	n/a	File
consensus	#main/consensus	n/a	File
consensus_af_threshold	#main/consensus_af_threshold	n/a	File
consensus_variants	#main/consensus_variants	n/a	File
coverage_depth	#main/coverage_depth	n/a	File
depth_threshold	#main/depth_threshold	n/a	File
failed_variant_sites	#main/failed_variant_sites	n/a	File
filter_failed_variants	#main/filter_failed_variants	n/a	File
low_cov_regions	#main/low_cov_regions	n/a	File
low_cov_regions_plus_filter_failed	#main/low_cov_regions_plus_filter_failed	n/a	File
low_cov_regions_plus_filter_failed_combined	#main/low_cov_regions_plus_filter_failed_combined	n/a	File
masking_regions	#main/masking_regions	n/a	File
multisample_consensus_fasta	#main/multisample_consensus_fasta	n/a	File
non_consensus_af_threshold	#main/non_consensus_af_threshold	n/a	File