I am working with ddRADseq data from harbor seal scat samples. There are not a lot of highly informative SNPs in my final panel and there are a lot of missing genotypes due to the degraded nature of the samples. I am about to sequence my samples again at a greater depth, however, I am trying to figure out my analysis pipeline with this initial data set.
The goal of this project is to be able to collect many samples from the field and identify any resampled seals. Therefore, I am trying to decide the best program for constructing genotypes and identifying any matches (I have three replicates of one seal). Programs like the R package Allelematch use product sizes, and I'm not sure if they can use SNP data (either ref/alt allele)? Additionally, GIMLET doesn't seem to be supported by the current version of Windows. A former student in my lab developed the program WISEPAIR, which could identify likely resamples, however that uses product sizes of microsatellites. I'm having a hard time finding a program that performs the type of multilocus comparisons I need.
Does anyone know any programs that may be able to use SNP data to perform multilocus pairwise comparisons to identify the unique genotypes in a set and therefore if there are any resampled individuals?