SNP calling in non-model organism

Question

[Janey]

hi I want to calling SNP in my RNAseq Data in my plant sample. my plant don't have reference genome. I de novo assembly my read. I want to use BWA and SAMTools softwares for SNP calling. Can anyone give me a good manual details for these two softwares?

Answer 1

[h.mon]

See this SAMtools workflow, has all you asked for and more.