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Just as the title says, I am working in PLINK 1.9 trying to convert the following VCF into a PLINK file (binary or not either is fine), while maintaining the SNP names from the VCF file. I am on Windows, so it would be easier for me to utilize PLINK for this. Does anyone know how to achieve this? The link below is the VCF file I am using.

I tried using the --vcf command by itself, along with using the --vcf command in conjunction with the --recode command. I also tried using the --double-id command to see if that would affect anything, but it did not.

http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz

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  • $\begingroup$ do you mean you've tried it already and it didn't preserve the SNP names? If so, please show which command you used. $\endgroup$
    – user438383
    Aug 18, 2022 at 8:17
  • $\begingroup$ Could you please explain why you need to convert a VCF file to PLINK format? I assume it's for another program, as VCF files can be read directly in PLINK. $\endgroup$
    – gringer
    Aug 19, 2022 at 8:55

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