HI,
I'm currently trying to create some synthetic data for testing purposes using a tooled called NEAT. However, i'm running into some confusion when the gene I'm trying to alter (cause a SNP in) is encoded on the antisense. When i look at my GBK file (of the bacteria i'm using as my reference) i want to alter the gene gid at position 69 changing an amino acid G to D. I also get the referring codon for this amino acid from the gbk which is GGT. Now i know that i simply need to alter the nucleotide G to A (producing the codon GAT) to get the alternate amino acid. However, when i create my VCF to do this i use the fasta file for this bacteria as my reference which is just the forwards strand so the nucleotides at the position i want to change are ACC so my VCF file is wrong and the program NEAT tells me that the REF nucleotide doesn't match the REF fasta.
Essentially what i'm asking is am i going to have to do this in a reverse manner and alter the forward codon to what i would want the reverse strand to be? SO altering the forward codon from ACC to ATC so the reverse codon goes from GGT to GAT giving me the desired outcome?
Apologies if that is all very confusing think i'm managed to get myself in a bit of a pickle
