Generic variation analysis reporting
Version 1

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Workflow Type: Galaxy

Stable

Generic variation analysis reporting

This workflow generates reports from a list of variants generated by Variant Calling Workflow.

The workflow accepts a single input:

A collection of VCF files

The workflow produces two outputs (format description below):

A list of variants grouped by Sample
A list of variants grouped by Variant

Here is example of output by sample. In this table all varinats in all samples are epxlicitrly listed:

Sample	POS	FILTER	REF	ALT	DP	AF	AFcaller	SB	DP4	IMPACT	FUNCLASS	EFFECT	GENE	CODON	AA	TRID	min(AF)	max(AF)	countunique(change)	countunique(FUNCLASS)	change
ERR3485786	11644	PASS	A	G	97	0.979381	0.907216	0	1,1,49,46	LOW	SILENT	SYNONYMOUS_CODING	D7L	tgT/tgC	C512	AKG51361.1	0.979381	1	1	1	A>G
ERR3485786	11904	PASS	T	C	102	0.990196	0.95098	0	0,0,51,50	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	D7L	Act/Gct	T426A	AKG51361.1	0.990196	1	1	1	T>C

Note the two alernative allele frequency fields: "AFcaller" ans "AF". LoFreq reports AF values listed in "AFcaller". They incorrect due to the known LoFreq bug. To correct for this we are recomputing AF values from DP4 and DP fields as follows: AF == (DP4[2] + DP4[3]) / DP.

Here is an example of output by variant. In this table data is aggregated by variant across all samples in which this variant is present:

POS	REF	ALT	IMPACT	FUNCLASS	EFFECT	GENE	CODON	AA	TRID	countunique(Sample)	min(AF)	max(AF)	SAMPLES(above-thresholds)	SAMPLES(all)	AFs(all)	change
11644	A	G	LOW	SILENT	SYNONYMOUS_CODING	D7L	tgT/tgC	C512	AKG51361.1	11	0.979381	1	ERR3485786,ERR3485787...	ERR3485786,ERR3485787,ERR3485789 ...	0.979381,1.0...	A>G
11904	T	C	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	D7L	Act/Gct	T426A	AKG51361.1	12	0.990196	1	ERR3485786,ERR3485787...	ERR3485786,ERR3485787,ERR3485789...	0.990196,1.0,1.0...	T>C

The workflow can be accessed at usegalaxy.org

The general idea of the workflow is:

SEEK ID: https://workflowhub.eu/workflows/354?version=1

Inputs

ID	Name	Description	Type
AF Filter	AF Filter	Allele Frequency Filter. This is the minimum allele frequency required for variants to be included in the reports.	float?
DP Filter	DP Filter	Depth Filter. This is the minimum depth of all alignments at a variant site.	int?
DP_ALT Filter	DP_ALT Filter	Depth Filter for variant allele. This is the minimum depth of alignments supporting a variant.	int?
Variation data to report	Variation data to report	Variation data in VCF format. Can be the output of any of the workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling	File[]

Steps

ID	Name	Description
4	SnpSift Filter	toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1
5	Compose text parameter value	toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
6	Compose text parameter value	toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
7	SnpSift Filter	toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1
8	SnpSift Extract Fields	toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0
9	Compute	toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6
10	Datamash	toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
11	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
12	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
13	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
14	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
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	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
18	Datamash	toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
19	Filter	Filter1
20	Datamash	toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
21	Join	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
22	Datamash	toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
23	Datamash	toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
24	Datamash	toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0
25	Join	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
26	Join	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
27	Cut	Cut1
28	Join	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
29	Cut	Cut1
30	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3
31	Cut	Cut1
32	Split file	toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0
33	Sort	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1
34	Sort	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1

Outputs

ID	Name	Description	Type
prefiltered_variants	prefiltered_variants	n/a	File
filtered_variants	filtered_variants	n/a	File
filtered_extracted_variants	filtered_extracted_variants	n/a	File
af_recalculated	af_recalculated	n/a	File
collapsed_effects	collapsed_effects	n/a	File
highest_impact_effects	highest_impact_effects	n/a	File
cleaned_header	cleaned_header	n/a	File
processed_variants_collection	processed_variants_collection	n/a	File
all_variants_all_samples	all_variants_all_samples	n/a	File
variants_for_plotting	variants_for_plotting	n/a	File
by_variant_report	by_variant_report	n/a	File
combined_variant_report	combined_variant_report	n/a	File