Hi there,
I am having trouble with my vcf files in R. These files were generated by custom perl wrappers that automate STACKS. For context, my study is a landscape pop-gen analysis of pest insects. At first, I could not load the finished files into R at all (30 000 loci unfiltered). I reduced the file down to 10 individuals (from >100), and the file will read into R now using the command:
>MPB10vcf=read.vcf('10_thinned.recode.vcf')
However, I can't seem to do anything with it now that it's there.
I would like to convert the vcf data into a genind object so I can run a PCA/DAPC and graph out the genetic structure. However, I am getting some different errors each time try to do this:
> MPB10_genind=vcfR2genind(MPB10vcf)
#Error in extract.gt(x) : ID column contains non-unique names
Does anyone have any thoughts/experiences with this?
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BeetleCheers •
I think this happened, here's an example row from my own data which triggers the same error:
Chrom1 3653 . A G 86 PASS NS=2 GT:DP 1/1:39 0/0:47 0/0:5 0/0:5 1/1:5 1/1:5 0/0:5 1/1:5 1/1:5 0/1:5 1/1:5 1/1:5 1/1:5 0/0:5 0/0:5 0/1:5 0/0:5 0/0:5 0/0:5 0/0:5 0/0:5
The third column is the ID column, which in my case is a dot for all SNPs! I have to replace these by something unique (Chrom+Position should work), then vcfR2genind should work too.
By the way, vcfR comes with its own vcf loading command, no need to use pegas' read.vcf: read.vcfR()
Thanks! I can load the modified file into R now, though I think there are still some troubles with how the original VCF file was generated. Ever forward!
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