Hello group,
In my work we create recombinant genomes for animal vaccination. I'm trying to characterize all the variations within all of our constructs and I have run into a problem. All of our constructs use the same backbone + a target gene of interest. I know where the insert is and the genome is stable so I inserted the correct sequences in the genomic location it is suppose to be and saved it as a fasta. The alignment and variant calling worked fine. I'm able to find variation without issue. My issue is now I want to classify the SNPs (synonymous, non-synonymous) and I can't.
Since the references are saved with their internal construct names, snpEff can't find the chromosome because they do not match. If I change the name I'm not sure if it will work any way because each genome has an extra 2000bp insert. compaire to the RefSeq that snpEff would pull from. I can make each individual genome in a custom database but they are unannotated fasta files.
So my question is what would be the best approach to do this? I'm currently thinking of making all the constructs into data sets for snpEff after annotating them and trying that. Is this the best way? Is there an easier way?
Any advice would be appreciated.
Thank you, Sean
