Hi All -

I'm using the R package PopGenome to analyze WGS data from a VCF file. I read in my VCF and GFF files by chromosome, as described [in this post][1]. Now I'd like to verify synonymous and non-synonymous substitutions using the `set.synnonsyn()` function. The `set.synnonsyn()` function has a `ref.chr = ` option, but I cannot find any details on what format the input chromosome should take when there are in fact multiple chromosomes in play. Should I feed the program a multifasta? Should I point it to a directory that contains individual chromosome fastas, similar to the way we import multiple VCF and GFF files? I've tried this every way I can think of but no luck.

Any help is much appreciated -

 [1]: https://www.biostars.org/p/121428/
Hi,

    test <- set.synnonsyn(test, ref.chr=c("chr1.fas","chr2.fas", ... ))

should work fine.

Best