EMUMADZ¶
Enhanced MUtation MApping and Detection in Zebrafish¶
Copyright © 2025 Tyrone Chen
, Richard Lupat , Michelle Meier , Maia Zethoven , Gregory Baillie , Scott Paterson , Oguzhan Baltaci , Cas Simons , Jason Li , Andrew Cox , Kelly Smith , Benjamin Hogan Code in this repository is provided under a MIT license. This documentation is provided under a CC-BY-4.0 license.
Visit our lab website here. Contact Benjamin Hogan at ben.hogan@petermac.org.
We thank Tyrone Chen, Richard Lupat , Michelle Meier , Maia Zethoven , Song Li , Niko Thio , and Jason Li from the Bioinformatics Core (RRID: `SCR_025901`) at the Peter MacCallum Cancer Centre for their helpful comments and contributions to the pipeline.Contains the documentation for our custom zebrafish whole genome sequencing pipeline.
Contents:
- Introduction
- Installation
- EMUMADZ pipeline case study 1
- BAM to SNP for F0-F2 comparisons
- Usage
- Data setup
- Whole zebrafish genome assembly
- Variant calling and read filtering
- Rename chromosomes in vcf with map file, and discard non-chromosomes
- Decompose multiallelic variants into individual instances
- Merge files with refs
- Filter for SNP only events
- Identify candidate SNPs
- Screen impact of SNP
- Visualising data
- Visualisation module
- EMUMADZ pipeline case study 2
- BAM to SNP for F2-F2 comparisons
- Usage
- Data setup
- Nextflow
- Whole zebrafish genome assembly
- Variant calling and read filtering
- Rename chromosomes in vcf with map file, and discard non-chromosomes
- Decompose multiallelic variants into individual instances
- Merge files with refs
- Filter for SNP only events
- Identify candidate SNPs
- Screen impact of SNP
- Visualising data
- Visualisation module
- EMUMADZ pipeline case study 3
- FASTQ to SNP for F2-F2 comparisons
- Usage
- Alignment
- Data setup
- Nextflow
- Whole zebrafish genome assembly
- Variant calling and read filtering
- Rename chromosomes in vcf with map file, and discard non-chromosomes
- Decompose multiallelic variants into individual instances
- Merge files with refs
- Filter for SNP only events
- Identify candidate SNPs
- Screen impact of SNP
- Visualising data
- Visualisation module
- API Reference
VCFParserVCFParser.calculate_allele_freq()VCFParser.create_bam_subset()VCFParser.create_reference_bam_subsets()VCFParser.generate_coverage_report()VCFParser.get_impact_color()VCFParser.get_relative_bam_file()VCFParser.match_sample()VCFParser.parse_ann_field()VCFParser.parse_csq_field()VCFParser.process_sample_variants()VCFParser.process_vcf()VCFParser.sample_infoVCFParser.validate_bam_subset()
main()HenkeScorerHomozygosityAnalyserHomozygosityErrorHomozygosityScorerVariantDataadd_homozygosity_to_variant_json()bedgraph_to_tdf()load_samplesheet()main()parse_allele_depths()write_bedgraph()
Appendix¶
Appendix: