Mapping And Molecular Identification Of Phenotype Causing Mutations
3.0

Workflow Type: Galaxy

Reproduce the tutorial analysis at https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html

Associated Tutorial

This workflows is part of the tutorial Mapping and molecular identification of phenotype-causing mutations, available in the GTN

Thanks to...

Tutorial Author(s): Wolfgang Maier

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
A. thaliana TAIR10 ref genome A. thaliana TAIR10 ref genome can be obtained from https://www.arabidopsis.org/download_files/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas
  • File
aligned reads from Ler mapping strain aligned reads from Ler mapping strain as obtained from https://zenodo.org/record/1098034/files/Ler_mapping_strain.bam
  • File
aligned reads from outcrossed F2 pool aligned reads from outcrossed F2 pool as obtained from https://zenodo.org/record/1098034/files/outcrossed_F2.bam
  • File

Steps

ID Name Description
3 SnpEff Download download the SnpEff genome annotation file corresponding to TAIR10 toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.1.0
4 Replace parts of text truncate ref genome chromosome names toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.1
5 MiModD Variant Calling compute variant call statistics for both samples across the entire genome toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varcall/0.1.8_1
6 MiModD Extract Variant Sites extract variants at sites for which at least one sample is not homozygous wildtype toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varextract/0.1.8_1
7 MiModD NacreousMap Variant allele frequency-based linkage analysis toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_map/0.1.8_1
8 MiModD VCF Filter get candidates in linked region toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_vcf_filter/0.1.8_1
9 SnpEff annotate the candidate mutations toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.1.0
10 MiModD Report Variants toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varreport/0.1.8_1

Version History

3.0 (earliest) Created 2nd Jun 2025 at 11:04 by GTN Bot

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Created: 2nd Jun 2025 at 11:04

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