text: user862: I'm new to data filtering on vcf data and vcftools.
  I performed variant calling on my dataset, CHR22, homo sapiens. I'd like to remove sites that are missing in more than 5% of individuals.  
  vcftools --missing-site --vcf updated_ids68.vcf
  
   
  This gives me a file with out.lmiss. That is missingness per locus.
  I had 68 individuals in my input vcf file.
  CHR     POS     N_DATA  N_GENOTYPE_FILTERED     N_MISS  F_MISS  
  22      16848278        106     0       30      0.283019  
  22      16848492        68      0       68      1  
  22      16849180        69      0       67      0.971014  
  22      16849229        68      0       68      1  
  22      16849376        133     0       3       0.0225564  
  22      16849476        132     0       6       0.0454545  
  22      16851734        126     0       36      0.285714  
  22      16852588        123     0       13      0.105691
  
   
  I'm unable to understand the output here. What does third column - N_DATA tell?
  133, 126 doesn't tell that this is number of individuals if my input had 68 individuals only.  
  VCFtools (0.1.15)
  fileformat=VCFv4.1
  
  user934: Humans are diploid, so you can expect to see up to 2*N (2*68=136) alleles, so N_DATA is the number of observances of that allele.
  
original_text: 862: <p>I'm new to data filtering on vcf data and vcftools.<br>
  I performed variant calling on my dataset, CHR22, homo sapiens. I'd like to remove sites that are missing in more than 5% of individuals.  </p>
  
  <pre><code>vcftools --missing-site --vcf updated_ids68.vcf
  </code></pre>
  
  <h1> </h1>
  
  <p>This gives me a file with out.lmiss. That is missingness per locus.<br>
  I had 68 individuals in my input vcf file.</p>
  
  <pre><code>CHR     POS     N_DATA  N_GENOTYPE_FILTERED     N_MISS  F_MISS  
  22      16848278        106     0       30      0.283019  
  22      16848492        68      0       68      1  
  22      16849180        69      0       67      0.971014  
  22      16849229        68      0       68      1  
  22      16849376        133     0       3       0.0225564  
  22      16849476        132     0       6       0.0454545  
  22      16851734        126     0       36      0.285714  
  22      16852588        123     0       13      0.105691
  </code></pre>
  
  <h1> </h1>
  
  <p>I'm unable to understand the output here. What does third column - <em>N_DATA</em> tell?<br>
  133, 126 doesn't tell that this is number of individuals if my input had 68 individuals only.  </p>
  
  <p>VCFtools (0.1.15)<br>
  fileformat=VCFv4.1</p>
   934: <p>Humans are diploid, so you can expect to see up to 2*N (2*68=136) alleles, so N_DATA is the number of observances of that allele.</p>
  