ploidy-aware-genotype-calling/main

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Workflow Type: Galaxy

This workflow performs variant and genotype calling on whole-genome paired-end sequencing data from organisms of any ploidy to produce annotated VCF and TSV files

SEEK ID: https://workflowhub.eu/workflows/2112?version=1

Inputs

ID Name Description Type
Annotation GTF Annotation GTF GTF with gene annotation, will be used for annotating variants
  • File
Paired Collection Paired Collection Illumina reads with fastqsanger encoding
  • File[]
Reference Genome fasta Reference Genome fasta Reference FASTA file to use as reference for variant calling
  • File
Set Ploidy for FreeBayes Variant Calling Set Ploidy for FreeBayes Variant Calling This step sets ploidy for FreeBayes Variant Caller
  • int

Steps

ID Name Description
4 fastp preprocessing Processing of FASTQ files toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.1.0+galaxy0
5 SnpEff build Build SnpEff database from the given reference fasta file toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy1
6 BWA-MEM mapping Mapping reads with reference sequence toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19
7 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+galaxy1
8 Samtools stats Generates statistics of BAM file toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.8
9 Mark Duplicates Marks duplicates in the input BAM file toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0
10 MultiQC Aggregation of results from mapping, and other preprocessing steps toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0
11 Variant Calling with FreeBayes Variant detection toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.10+galaxy1
12 Post processing of FreeBayes Call Processes output data from FreeBayes variant caller toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.22+galaxy0
13 SnpEff annotations Annotates detected variants toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy1
14 Extract using SnpSift Extracts required fields from the VCF file toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0
15 Collapse Collapse multiple datasets into a single dataset 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
Preprocessing and mapping reports Preprocessing and mapping reports n/a
  • File
output_vcf output_vcf n/a
  • File
SnpEff eff reports SnpEff eff reports n/a
  • File
SnpEff variants SnpEff variants n/a
  • File
Annotated Variants Annotated Variants n/a
  • File

Version History

v0.1.2 (latest) Created 25th Apr 2026 at 03:01 by WorkflowHub Bot

Updated to v0.1.2


Frozen v0.1.2 d0ca1eb

v0.1.1 (earliest) Created 13th Mar 2026 at 03:01 by WorkflowHub Bot

Updated to v0.1.1


Frozen v0.1.1 17e625a
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License
MIT License (MIT)
Activity

Views: 665   Downloads: 5589   Runs: 1

Created: 13th Mar 2026 at 03:01

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