generic-variant-calling-wgs-pe/main
v0.1

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Run on Galaxy

This workflow does not specify a "main" workflow file.

Workflow Type: Galaxy

Tests All failing

Generic variation analysis on WGS PE data

This workflows performs paired end read mapping with bwa-mem followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff. The reference genome can be provided as a GenBank file.

SEEK ID: https://workflowhub.eu/workflows/357?version=1

Inputs

ID	Name	Description	Type
GenBank genome	#main/GenBank genome	GenBank with annotations for the genome of interest	File
Name for genome database	#main/Name for genome database	Should describe your reference genome, e.g. mpxv for Monkeypox virus.	string
Paired Collection	#main/Paired Collection	Illumina reads with fastqsanger encoding	array containing File

Steps

ID	Name	Description
3	fastp	toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0
4	SnpEff build:	toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4
5	Map with BWA-MEM	toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2
6	Samtools view	toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy1
7	MarkDuplicates	toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2
8	Samtools stats	toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
9	Realign reads	toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
10	MultiQC	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0
11	Insert indel qualities	toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0
12	Call variants	toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1
13	Lofreq filter	toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0
14	SnpEff eff:	toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1

Outputs

ID	Name	Description	Type
Fasta sequences for genbank file	#main/Fasta sequences for genbank file	n/a	File
SnpEff eff: stats	#main/SnpEff eff: stats	n/a	File
SnpEff variants	#main/SnpEff variants	n/a	File
SnpEff4.3 database	#main/SnpEff4.3 database	n/a	File
bwa_mem_alignments	#main/bwa_mem_alignments	n/a	File
called_variants	#main/called_variants	n/a	File
fastp_html_report	#main/fastp_html_report	n/a	File
fastp_pe	#main/fastp_pe	n/a	File
filtered_alignment	#main/filtered_alignment	n/a	File
mapped_reads_stats	#main/mapped_reads_stats	n/a	File
markduplicates_reads	#main/markduplicates_reads	n/a	File
markduplicates_stats	#main/markduplicates_stats	n/a	File
preprocessing_and_mapping_reports	#main/preprocessing_and_mapping_reports	n/a	File
realigned_deduplicated_filtered_mapped_reads	#main/realigned_deduplicated_filtered_mapped_reads	n/a	File
realigned_deduplicated_filtered_mapped_reads_with_indel_quals	#main/realigned_deduplicated_filtered_mapped_reads_with_indel_quals	n/a	File
soft_filtered_variants	#main/soft_filtered_variants	n/a	File