haploid-variant-calling-wgs-pe/main

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Workflow Type: Galaxy

Workflow for variant analysis against a reference genome in GenBank format

SEEK ID: https://workflowhub.eu/workflows/1190?version=2

Inputs

ID Name Description Type
Annotation GTF Annotation GTF GTF with gene annotation, will be used for annotating variants
  • File
Genome fasta Genome fasta Fasta file to use as reference for variant calling
  • File
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/1.3.5+galaxy0
4 SnpEff build: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.4+galaxy0
5 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19+galaxy1
6 Samtools view Retains alignments if read is paired and mapped in proper orientation toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy2
7 Samtools stats toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.9
8 MarkDuplicates toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0
9 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy1
10 Realign reads toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
11 Call variants toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy3
12 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3
13 SnpEff eff: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.4+galaxy0
14 SnpSift Extract Fields toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/5.4.0c+galaxy0
15 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0

Outputs

ID Name Description Type
fastp html report fastp html report n/a
  • File
SnpEff4.3 database SnpEff4.3 database n/a
  • File
Preprocessing and mapping reports Preprocessing and mapping reports n/a
  • File
SnpEff variants SnpEff variants n/a
  • File
SnpEff eff reports SnpEff eff reports n/a
  • File
Annotated Variants Annotated Variants n/a
  • File

Version History

v0.2 (latest) Created 7th Jul 2026 at 03:02 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 88fd52c

v0.1 (earliest) Created 30th Oct 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 963ebf4
help Creators and Submitter
Creator
Submitter
Tools
fastp
BWA
SAMtools
MultiQC
lofreq
License
MIT License (MIT)
Activity

Views: 4045   Downloads: 8737   Runs: 0

Created: 30th Oct 2024 at 03:02

Annotated Properties
Scientific disciplines
Computer Science
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