Post date: May 21, 2020 9:40:51 PM
Overall goal: study the Friends dataset to see if there is any spatial patterning within clones
Is IBD mapping different from linkage mapping?
Paper suggests Identity By Descent analysis to distinguish clones from non-clones in Friends. IBD means that a DNA segment that is found in two or more individuals was inherited from a common ancestor without recombination (clonal?)
This paper uses PLINK to do the IBS analysis:https://zzz.bwh.harvard.edu/plink/data.shtml#map
To do the IBS analysis, I need a .map file of the dataset, which is the mapping of all SNPs on the genome (can this work with a scattered reference genome?)
Linkage map for GBS:
paper to read using GBS in almond: https://www.g3journal.org/content/8/1/161
tutorial: https://bioinformaticsworkbook.org/dataAnalysis/GenomeAssembly/GeneticMaps/creating-genetic-maps.html
IBD mapping using cancer data: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342326/