Generic variation analysis on WGS PE data
Version 1

Workflow Type: Galaxy
Stable

Generic variant calling

A generic workflow for identification of variants in a haploid genome such as genomes of bacteria or viruses. It can be readily used on MonkeyPox. The workflow accepts two inputs:

  • A genbank file with the reference genomes
  • A collection of paired fastqsanger files

The workflow outputs a collection of VCF files for each sample (each fastq pair). These VCF files serve as input to the Reporting workflow.

Workflow can be accessed directly on usegalaxy.org

The general idea of the workflow is:

Inputs

ID Name Description Type
Paired Collection Paired Collection Illumina reads with fastqsanger encoding n/a
GenBank genome GenBank genome n/a n/a
reads reads runtime parameter for tool Call variants n/a
reference_source reference_source runtime parameter for tool Call variants n/a
invcf invcf runtime parameter for tool Lofreq filter n/a
intervals intervals runtime parameter for tool SnpEff eff: n/a
transcripts transcripts runtime parameter for tool SnpEff eff: n/a

Steps

ID Name Description
0 Paired Collection Illumina reads with fastqsanger encoding
1 GenBank genome
2 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0
3 SnpEff build: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4
4 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
5 Samtools view toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2
6 Samtools stats toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
7 MarkDuplicates toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2
8 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1
9 Realign reads toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
10 Insert indel qualities toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0
11 Call variants toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0
12 Lofreq filter toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0
13 SnpEff eff: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1

Outputs

ID Name Description Type
output_paired_coll output_paired_coll n/a
report_html report_html n/a
report_json report_json n/a
snpeff_output snpeff_output n/a
output_fasta output_fasta n/a
bam_output bam_output n/a
outputsam outputsam n/a
output output n/a
metrics_file metrics_file n/a
outFile outFile n/a
stats stats n/a
html_report html_report n/a
realigned realigned n/a
output output n/a
variants variants n/a
outvcf outvcf n/a
snpeff_output snpeff_output n/a
statsFile statsFile n/a

Version History

Version 1 (earliest) Created 1st Jun 2022 at 13:46 by Anton Nekrutenko

Initial commit


Open master 9738be7
help Creators and Submitter
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Additional credit

Wolfgang Maier

Submitter
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Views: 582

Created: 1st Jun 2022 at 13:46

Last updated: 1st Jun 2022 at 16:51

Last used: 28th Nov 2022 at 03:42

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