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