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

Workflow Type: Galaxy

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.

Inputs

ID Name Description Type
GenBank genome GenBank genome GenBank with annotations for the genome of interest
  • File
Name for genome database Name for genome database Should describe your reference genome, e.g. mpxv for Monkeypox virus.
  • string
Paired Collection Paired Collection Illumina reads with fastqsanger encoding
  • 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
fastp_pe fastp_pe n/a
  • File
fastp_html_report fastp_html_report n/a
  • File
SnpEff4.3 database SnpEff4.3 database n/a
  • File
Fasta sequences for genbank file Fasta sequences for genbank file n/a
  • File
bwa_mem_alignments bwa_mem_alignments n/a
  • File
filtered_alignment filtered_alignment n/a
  • File
markduplicates_stats markduplicates_stats n/a
  • File
markduplicates_reads markduplicates_reads n/a
  • File
mapped_reads_stats mapped_reads_stats n/a
  • File
realigned_deduplicated_filtered_mapped_reads realigned_deduplicated_filtered_mapped_reads n/a
  • File
preprocessing_and_mapping_reports preprocessing_and_mapping_reports 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
SnpEff eff: stats SnpEff eff: stats n/a
  • File
SnpEff variants SnpEff variants n/a
  • File

Version History

v0.1 (earliest) Created 4th Jun 2022 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 10e094e
help Creators and Submitter
Creators
Not specified
Additional credit

Anton Nekrutenko

Submitter
License
Activity

Views: 2006   Downloads: 111

Created: 4th Jun 2022 at 03:01

help Tags
help Attributions

None

Total size: 1.01 MB
Powered by
(v.1.15.0)
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH