MiModD - Identify a phenotypic mutation in A. thaliana

Annotation: Reproduce the tutorial analysis at http://galaxyproject.github.io/training-material/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html

StepAnnotation
Step 1: Input dataset
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can be obtained from https://www.arabidopsis.org/download_files/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas
Step 2: Input dataset
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as obtained from https://zenodo.org/record/1098034/files/outcrossed_F2.bam
Step 3: Input dataset
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as obtained from https://zenodo.org/record/1098034/files/Ler_mapping_strain.bam
Step 4: SnpEff Download
athalianaTair10
download the SnpEff genome annotation file corresponding to TAIR10
Step 5: Replace
Output dataset 'output' from step 1
^>(\w+).*
>chr$1
True
False
False
False
entire line
truncate ref genome chromosome names
Step 6: MiModD Variant Calling
Use a genome from my history
Output dataset 'outfile' from step 5
Output dataset 'output' from step 2,Output dataset 'output' from step 3
False
More options:
True
250
compute variant call statistics for both samples across the entire genome
Step 7: MiModD Extract Variant Sites
Output dataset 'ofile' from step 6
include information from pre-calculated vcf datasets
False
extract variants at sites for which at least one sample is not homozygous wildtype
Step 8: MiModD NacreousMap
Variant Allele Frequency Mapping
VCF file of variants (for de-novo mapping)
Output dataset 'output_vcf' from step 7
Yes
outcrossed F2
Empty.
Ler
False
Empty.
bin sizes to analyze variants in (defaults to: 1Mb and 500Kb)s
Give me everything (scatter plots and histograms)
True
0.0
1.0
preserve relative contig sizes
0.1
histogram colors
custom scatter plot colors
Do not generate per-variant output
Variant allele frequency-based linkage analysis
Step 9: MiModD VCF Filter
Output dataset 'output_vcf' from step 7
Sample-specific Filters
Sample-specific Filter 1
outcrossed F2
1/1
0
0
Empty.
Sample-specific Filter 2
Ler
0/0
0
0
Empty.
Region Filters
Region Filter 1
chr2
18000000
19000000
all types of variants
Empty.
get candidates in linked region
Step 10: SnpEff
Output dataset 'outputfile' from step 9
VCF
VCF (only if input is VCF)
Reference genome from your history
Output dataset 'snpeff_db' from step 4
Unavailable.
Unavailable.
5000 bases
2 bases
Use Defaults
Use 'EFF' field compatible with older versions (instead of 'ANN').
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Nothing selected.
No
Use default (based on input type)
Empty.
False
True
annotate the candidate mutations
Step 11: MiModD Report Variants
Output dataset 'snpeff_output' from step 10
HTML
A. thaliana
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