Extra scripts
The scripts listed below can be found in the scripts/ directory and you may find them to be useful. None of these scripts are used by LepMak3r.
This simple script extracts contig and position information from the data_f.call.gz file generated from running the first steps of the pipeline (ParentCall2 and Filtering2) into the file snps.txt.
This is a loop that takes a given map from the maps.splitchrom folder and iterates over a range of LOD scores to try to split out a specific linkage group that may be overclustered. It's fairly well annotated, so adjust it to your needs.
The same as map_summary.sh used by LepMak3r to make maps.summary.txt for visual inspection, except it acts on the refined maps you would make using refine_map.sh.
If you have a simple single-family cross, you can use popmap2pedigree to convert your Stacks or dDocent generated popmap file into a LepMap3-compliant pedigree file. Make sure your popmap is a tab-separated two-column text file with the first column of sample names and the second column of parent or progeny designations:
sample_1<tab>parent
sample_2 parent
f1_001 progeny
f1_002 progeny
f1_003 progeny
etc...
So long as the parents are designated parent, it doesn't matter what progeny are designated as. Go wild 😃
(... but like, not too wild)
This is a simple bash script that concatenates the distance intervals files in intervals into a single file necessary to feed into the Lep-Anchor wrapper lepanchor_wrapper.sh (part of Lep-Anchor, not included). It should be run in the intervals folder and the only argument is the markers file that can be obtained from extract_markers.sh. Note: LepMak3r does not run Lep-Anchor.
This python3 script converts Lep-Map3 distances output into ALLMAPS format. Run it without arguments to see the usage text. Note: LepMak3r does not run ALLMAPS.
