Hi everyone, i am bit new in the field of genomics, i am having problem in converting my .vcf file to plink bed format through plink. i have to use plink bed file for estimation of population structure through faststructure
Hello, There are multiple tools out there to convert a VCF to PLINK binary format, namely the .bed, .bim. and .fam files of the 'binary fileset'.
See link below for more info.
https://www.biostars.org/p/313943/
Good luck!
You should use PLINK for this conversation process.
plink --vcf [insert your vcf name here] --out [intended name for binary files]
This code above should give you the files.
https://www.cog-genomics.org/plink/1.9/data
Plink does the conversion easily. What is the problem exactly? Are you having error messages? If so, what are they?
to make binary file from a vcf file, please try following command:
plink --vcf file.vcf.gz --const-fid
The following command can be used:
plink --vcf file.vcf(.gz) --make-bed --out fileout
I am trying to convert a vcf file in the form of vCard into Plink format using Plink. But I get a error message showing "No samples in vcf file". When I open the vcf file in text editor I can see the information listed. Cannot figure out the problem.