Body: <p>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.</p>
  <p>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.</p>
  <p><a href="http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz" rel="nofollow noreferrer">http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz</a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-08-18T08:17:02.170Z
Comments.Text: do you mean you've tried it already and it didn't preserve the SNP names? If so, please show which command you used.
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-08-19T08:55:23.297Z
Comments.Text: 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](https://www.cog-genomics.org/plink/1.9/input#vcf).
Comments.UserDisplayName: gringer
Tags: <vcf><snp><plink>
Title: Converting from VCF to PLINK while maintaining the SNP names from the VCF file
ThreadText: # Converting from VCF to PLINK while maintaining the SNP names from the VCF file
  
  (Asked by: username_0 on 2022-08-18)
  
  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>
  
  **Tags:** vcf, snp, plink
  
  > **Comments:**
  > **username_1**: do you mean you've tried it already and it didn't preserve the SNP names? If so, please show which command you used.  
  > **username_2**: 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](https://www.cog-genomics.org/plink/1.9/input#vcf).  
  
  ---
  
  ## 0 answers
  
  