sars-cov-2-consensus-from-variation/COVID-19-CONSENSUS-CONSTRUCTION
v0.1

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 a list of variants. Hard-mask regions with low coverage and sites with called, but filtered variants. Note: Sites with called and retained variants are never masked.

SEEK ID: https://workflowhub.eu/workflows/138?version=6

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/2.29.2
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	VCFtoTab-delimited:	toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0
14	SnpSift Filter	toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1
15	Cut	Cut1
16	VCFtoTab-delimited:	toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0
17	Compute	toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6
18	Cut	Cut1
19	Compute	toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6
20	Compute	toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6
21	Cut	Cut1
22	Compute	toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6
23	Cut	Cut1
24	Concatenate	toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1
25	Merge	toolshed.g2.bx.psu.edu/repos/devteam/merge/gops_merge_1/1.0.0
26	Subtract	toolshed.g2.bx.psu.edu/repos/devteam/subtract/gops_subtract_1/1.0.0
27	Compute	toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6
28	bedtools MaskFastaBed	toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.29.2
29	Cut	Cut1
30	bcftools consensus	toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10
31	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2

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
called_variants_table	#main/called_variants_table	n/a	File
chrom_pos_ref_called_variants	#main/chrom_pos_ref_called_variants	n/a	File
chrom_pos_ref_called_variants_with_0_based_start	#main/chrom_pos_ref_called_variants_with_0_based_start	n/a	File
chrom_pos_ref_called_variants_with_0_based_start_end	#main/chrom_pos_ref_called_variants_with_0_based_start_end	n/a	File
chrom_pos_ref_failed_variants	#main/chrom_pos_ref_failed_variants	n/a	File
chrom_pos_ref_failed_variants_with_0_based_start	#main/chrom_pos_ref_failed_variants_with_0_based_start	n/a	File
chrom_pos_ref_failed_variants_with_0_based_start_end	#main/chrom_pos_ref_failed_variants_with_0_based_start_end	n/a	File
consensus	#main/consensus	n/a	File
consensus_variants	#main/consensus_variants	n/a	File
coverage_depth	#main/coverage_depth	n/a	File
failed_variant_sites	#main/failed_variant_sites	n/a	File
failed_variants_table	#main/failed_variants_table	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
masked_preconsensus	#main/masked_preconsensus	n/a	File
masking_regions	#main/masking_regions	n/a	File
masking_regions_with_1_based_start	#main/masking_regions_with_1_based_start	n/a	File
multisample_consensus_fasta	#main/multisample_consensus_fasta	n/a	File
non_consensus_variants	#main/non_consensus_variants	n/a	File