error while accessing a vcf file

[sekhwal]

Hi,
I have a vcf file. It is filtered by tassel and save it as vcf.

while accessing the this vcf file to popgenInfo with the following commands, I am getting the following error. Please help me to figure out the issue.

gi_vcf <- read.vcfR( file = "gi-filter-new.vcf", verbose = T )
gi_genind <- vcfR2genind(gi_vcf)

error::::;
Error in extract.gt(x, return.alleles = return.alleles) :
ID column contains non-unique names

[sekhwal]

I used my unfiltered file and I did not get the above error.
I used following commands: However, when I write the .txt file it is taking very long time to generate file. Is there any way I can filter the input vcf file?

gi_genind <- vcfR2genind(gi_vcf)
class(gi_genind)
gi_genind
gi_genclone <- poppr::as.genclone(gi_genind)
gi_genclone

write.table(gi_genclone, file = "gi_vcfR.txt", sep = "\t",
row.names = TRUE, col.names = NA)

[zkamvar]

You might benefit from the documentation for vcfR on this matter: https://knausb.github.io/vcfR_documentation/filtering_data.html

Otherwise, if you are still having issues, the best place to ask search for answers or ask questions would be the developer's GitHub page: https://github.com/knausb/vcfR/issues