What to expect from LepMap3 via LepWrap
So you understand what to expect during a run, here is what the working directory should look like before you start. Notice that you will need to provide the filtered vcf and pedigree files. You can name them whatever you want, as long as you use their correct names in the config.yaml.
Folder_name
├── config.yaml
├── filtered_data.vcf
├── pedigree_file.txt
├── LepWrap
├── software # directory of the LepMap/LepAnchor modules
├── rules # directory of the rule files
├── scripts # directory of misc helpful scripts
When LepWrap finishes, your directory structure will look like this (most files omitted for clarity):
Folder_name
├── 1_ParentCall
│ └── data.lepmap3.gz
├── 2_Filtering
│ └── data.filtered.lepmap3.gz
├── 3_SeparateChromosomes
├── 4_OrderMarkers
│ └── logs
│ ├── logs
│ ├── recombination
├── 5_Trim
│ └── logs
│ └── plots
├── 6_OrderMarkers
│ └── logs
│ ├── logs
│ ├── recombination
├── 7_Distances
├── 7_DistancesSexAverage
│ └── logs
├── 7_Intervals
│ └── logs
├── software
├── rules
├── scripts
