Dear reader, I am working on non-model organism and I have discovered a set of SNP's and indels by aligning my RNAseq data to it's reference transcriptome. Now, I am interested to map these SNP's. How can this be done??I do have a closely related Genome however it is not finished. I have been suggested to use synteny based approach will someone please try and address this question??
Thanking you all in advance