Hi, I have reads from a plant species. I want to identify to which lineage (subspecies) my reads belongs based on distinct variants found in genome representatives of these different lineages. Ex: T at postion 3 in lineages 1, C at position 3 in lineage 2 - Reads : C at these position, probably lineage 2.
I mapped my reads to a reference and called SNPs. I want to look if some of these SNPs are found in the other genome. The problem is that postion are not identical between reference genome. Any idea about how I can deal with that ?
I tried to align my different genomes to identify lineage-specific SNP but as gaps are created, they can't be compared to my other list.