text: user1837: I have a list of SNPs (index SNPs). As my tagging SNPs, I want to use SNP data from here. The data has the following column headers: Chromosome, Position, MarkerName, Effect_allele,   Non_Effect_allele, Beta, SE, Pvalue.
  My ultimate aim is to identify SNPs in the tagging set that are in LD with each of index SNPs. I need to calculate r2 between index SNPs and tagging SNPs within 1MB window and get a table of index vs tagging SNPs (r2>0.8). 
  How can I use PLINK to carry out this work? I'm new to PLINK and LD clumping
  
  user73: You can't generate LD statistics for summary data from SNPs, as the LD calculation relies on the comparison of variants at the genotype level. Plink expects data to be in a genotype matrix with either each marker for each line (probably better in your case), or each individual for each line. Plink v1.9, in particular, will accept VCF-formatted input files, when populated with 'GT' information that describes the variants for each individual.
  If you're okay with using the 1000 genome population for calculating LD, plink v1.9-compatible datasets should be accessible from
  here.
  If not, you'll need to discuss your project with IGAP to see if you can have access to genotype-level data for LD testing. That's unlikely, because there are personal identification issues associated with non-summary data.
  There's comprehensive documentation about the LD command(s) on the Plink 1.9 website here.
  
original_text: 1837: <p>I have a list of SNPs (index SNPs). As my tagging SNPs, I want to use SNP data from <a href="http://web.pasteur-lille.fr/en/recherche/u744/igap/igap_download.php" rel="nofollow noreferrer">here</a>. The data has the following column headers: Chromosome, Position, MarkerName, Effect_allele,   Non_Effect_allele, Beta, SE, Pvalue.</p>
  
  <p>My ultimate aim is to identify SNPs in the tagging set that are in LD with each of index SNPs. I need to calculate r2 between index SNPs and tagging SNPs within 1MB window and get a table of index vs tagging SNPs (r2>0.8). </p>
  
  <p>How can I use PLINK to carry out this work? I'm new to PLINK and LD clumping</p>
   73: <p>You can't generate LD statistics for summary data from SNPs, as the LD calculation relies on the comparison of variants at the genotype level. Plink expects data to be in a genotype matrix with either each marker for each line (probably better in your case), or each individual for each line. Plink v1.9, in particular, will accept VCF-formatted input files, when populated with 'GT' information that describes the variants for each individual.</p>
  
  <p>If you're okay with using the 1000 genome population for calculating LD, plink v1.9-compatible datasets should be accessible from
  <a href="https://www.cog-genomics.org/plink2/resources" rel="nofollow noreferrer">here</a>.</p>
  
  <p>If not, you'll need to discuss your project with IGAP to see if you can have access to genotype-level data for LD testing. That's unlikely, because there are personal identification issues associated with non-summary data.</p>
  
  <p>There's comprehensive documentation about the LD command(s) on the Plink 1.9 website <a href="https://www.cog-genomics.org/plink/1.9/ld" rel="nofollow noreferrer">here</a>.</p>
  