How can I use PopGenome set.synnonsyn() function on whole genome vcf data?

Question

[apc]

Hi everyone.

I would like to use PopGenome to calculate genome-wide Pn/Ps-ratio starting with a whole Genome-VCF file. I managed to do this for genes in candidate windows using PopGenome. But for the whole genome it did not work. When I try to verify synonymous and non-synonymous SNP's using the set.synnonsyn() function the output I get is not right, although the command runs without any error or warning. I think the problem is that I have several contigs. Maybe someone ran into the same issue and found a solution or a workaround. Here is the code I used (R version 3.6.0, PopGenome_2.7.5):

read in the VCF file:

genome<-readData("VCFScaffolds/", format="VCF", gffpath="GFFScaffolds", include.unknown=TRUE)

I have 10 chromosomes:

[e-mail]

Output: [1] "000008F|quiver" "000010F|quiver" "000016F|quiver" "000022F|quiver" [5] "000032F|quiver" "000037F|quiver" "000040F|quiver" "000045F|quiver" [9] "000047F|quiver" "000058F|quiver"

Now set syn. and nonsyn. SNPs:

genome_sNs<-set.synnonsyn(genome, ref.chr=genome.fasta)

Split data into coding sequences:

genome_sNs_split<-splitting.data(genome_sNs, subsites="coding", whole.data=FALSE)

Calculate diversity stats for all SNPs and syn. and nonsyn. SNPs separately

genome_sNs_split<-diversity.stats(genome_sNs_split)
genome_sNs_split_ns<-diversity.stats(genome_sNs_split, subsites="nonsyn")
genome_sNs_split_syn<-diversity.stats(genome_sNs_split, subsites="syn")

Extract nucleotide diversities

nuc_div_all<[e-mail][,1]
nuc_div_ns<[e-mail][,1]
nuc_div_syn<[e-mail][,1]

When I now compare the nucleotide diversity of gene_1 obtained from the whole genome analysis, like described here to the nucleotide diversity of gene_1 obtained from the candidate analysis where I read in a 12kb window via the read.VCF() function they match for all sites (nuc_div_all) but NOT for syn (nuc_div_ns), and nonsyn. (nuc_div_ns) subsites!

Does anyone have any idea what the problem might be? Any hints and ideas are appreciated!