Given a list of samples that can be used to construct the allelic ladder, this script will give a selection of samples that cover alleles found in the greater population

Two files are needed:

-- A tab-delimited file with sample names in the first column, followed by two columns (allele A and B) for each genotyped locus. There should be no column headers. e.g.

COC20020503-0012	120	130	158	158	201	205	79	79	131	135	183	187	140	143	182	182	134	156	221	221	147	147	121	121	96	129
COC20020504-0023	120	130	158	158	201	205	79	79	131	135	183	187	140	143	182	182	134	156	221	221	147	147	121	121	96	129
COC20020504-0013	120	120	154	158	201	203	79	79	131	131	177	183	140	145	182	186	160	160	224	235	145	147	119	119	125	131
COC20020504-0025	120	120	154	158	201	203	79	79	131	131	177	183	140	145	182	186	160	160	224	235	145	147	119	119	125	131
COC20020504-0015	120	120	154	156	201	203	79	81	131	137	183	185	140	143	182	182	160	160	211	233	145	147	117	121	120	120

-- A text file with the samples availables to act as an allelic ladder, each sample on a new name. The names should be identical to how they appear in the original tab-delimited file with all the genotypes e.g.

PmaNZ010
PmaNZ011
PmaNZ058
PmaNZ060
PmaNZ_U07-099

To run the Rscript, paste it into your R console and then execute by:

allelic_ladder(working_dir,tabdelim_file,allelic_ladder_samples, end_allele_weight)
# e.g. allelic_ladder("C:/Users/Alana/Downloads","Sperm_whale_DNA_profile_sample_name_loci.txt","NZsamplenames.txt")

where end_allele_weight reflects the weight to be placed on retaining the maxmimum and minimum (in size) alleles for each locus (remaining alleles are retained roughly in order of their frequency as the number of samples included in the allelic ladder is reduced). The higher this number, the more retaining the max and minimum sized allele for each locus will be prioritized.

You can also run this on a locus by locus basis by deleting the columns that do not pertain to your locus of interest. This could be useful if you are planning on sending amplicons for between lab standardization rather than whole DNA.

Wrote this code to faciliate a collaboration between labs needing to establish a common allelic ladder. I am no longer actively maintaining this repository, but will respond to issues.