R: poppr: Problems converting vcf to genclone object

Question

[evolozzy]

I can convert VCF to genclone by reading vcf data with vcfR, converting to into genind and then into genclone object in two separate ways, however, each conversion results in a different problem.

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Method 1

genIndObj<-vcfR2genind(vcf,ploidy=1,strata=Loc)
genCloneObj<-as.genclone(genIndObj)

Problem with method 1

When I look at the locus table with locus_table(genCloneObj) I get only one allele in each locus, even though there are 2.

info_table(genCloneObj,type="missing",plot=T) works fine, I can see all missing loci information.

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Method 2

genIndObj<-vcfR2genind(vcf,ploidy=1,strata=Loc)
genind2genalex(genIndObj,filename ="genalex.xls")
genCloneObj<-read.genalex("genalex.xls")

Problem with method 2

In this one locus_table(genCloneObj) works as expected.

However I lose some loci, and all missing loci information. when I run info_table(genCloneObj,type="missing",plot=T) I get NULL.

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I'd really appreciate some help converting vcf to genclone.

Answer 1

[evolozzy]

I've found a solution, using pegas withvcfR.

This causes another problem but it is easy to come up with a workaround. While reading vcf files with read.vcf the positions of the SNPs might not be read, so I get that information using getPOS and put that into the data frame created by pegas.

vcf<-read.vcf(vcf.file) 
vcfR<-read.vcfR(vcf.file)
colnames(vcf)<-getPOS(vcfR)
genIndObj<-loci2genind(vcf,ploidy=1)
strata(genIndObj)<-strata.df
setPop(genIndObj)<-~pop/subPop
genCloneObj<-as.genclone