Extra scripts
The scripts below aren't used by LepWrap, but you may find them useful.
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. The only argument is specifying the data file.
This is a "hard filter" where you set a maximum number of allowed linkage groups and any markers assigned to a linkage group greater than that will be converted to a single (i.e. linkage group 0). In other words, if you expect 20 linkage groups for your species, you can set the cutoff to 20, and any markers in linkage groups 21+ will be reassigned to 0. Useful right before the JoinSingles2All module.
This is a loop that takes a given map from Lep-Map3 SeparateChromosomes2 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. Calls MapSummary.r at the end to generate a summary table.
A convenient way to view the usage/help text of the LepMap/LepAnchor modules.
A very experimental script that filters out errant markers from a linkage group by drawing splines over your linkage map and performing 3 sliding windows of 2 different resolutions to apply penalties to markers that are outliers (2 x mean of local residuals) in that window. It's kinda complicated. If you plan on using this, you need to consider if filtering markers in this way is just cherry-picking data or is analytically/biologically justifiable. I have not employed this in my own work.
Similar to refine_map.sh, this will loop over a range of LOD limit values (and a fixed LOD difference threshold) to try assigning your singles (markers assigned to LG 0) into the available linkage groups with the JoinSingles2All Lep-Map3 module. I recommend using purge_lg.sh to hard-filter your mapfile before doing this.
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 shouldn'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.
This python3 script converts Lep-Map3 distances output into ALLMAPS format. Run it without arguments to see the usage text. Note: LepWrap does not run ALLMAPS.
