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
GenBank genome GenBank genome n/a
  • File
Paired Collection Paired Collection Illumina reads with fastqsanger encoding
  • File[]

Steps

ID Name Description
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
fastp_pe fastp_pe n/a
  • File
fastp_html_report fastp_html_report n/a
  • File
SnpEff4.3 database for SnpEff4.3 database for n/a
  • File
Fasta sequences for Fasta sequences for n/a
  • File
Map with BWA-MEM on input dataset(s) (mapped reads in BAM format) Map with BWA-MEM on input dataset(s) (mapped reads in BAM format) n/a
  • File
filtered_mapped_reads filtered_mapped_reads n/a
  • File
mapped_reads_stats mapped_reads_stats n/a
  • File
markduplicates_reads markduplicates_reads n/a
  • File
markduplicates_stats markduplicates_stats n/a
  • File
preprocessing_and_mapping_reports preprocessing_and_mapping_reports n/a
  • File
realigned_deduplicated_filtered_mapped_reads realigned_deduplicated_filtered_mapped_reads n/a
  • File
realigned_deduplicated_filtered_mapped_reads_with_indel_quals realigned_deduplicated_filtered_mapped_reads_with_indel_quals n/a
  • File
called_variants called_variants n/a
  • File
soft_filtered_variants soft_filtered_variants n/a
  • File
_anonymous_output_1 _anonymous_output_1 n/a
  • File
SnpEff eff: on input dataset(s) - stats SnpEff eff: on input dataset(s) - stats n/a
  • File

Version History

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

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Open master 9738be7
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Additional credit

Wolfgang Maier

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Views: 3053   Downloads: 294

Created: 1st Jun 2022 at 13:46

Last updated: 1st Jun 2022 at 16:51

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