I'm a student who is new to this aspect of bioinformatics in my work. I deeply apologize if this is a silly question. But I'm stuck at the point where the analysis for the variants are done. I see that lots of work are done for human genome. But I want to analyze variants from Arabidopsis.
What I have done so far : identified and extracted the SNPs (in vcf format) from accessions for Arabidopsis for a protein coding gene
What I want to do: Map those back in to a reference gene/or genome (I have both) I have downloaded and convert it to an amino acid sequence to see whether the nucleotide polymorphism has an effect on the amino acid sequence
Can you please help? Thanks a lot.