3
$\begingroup$

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

$\endgroup$
4
$\begingroup$

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.

$\endgroup$
  • 1
    $\begingroup$ Furthermore, it also looks like N_MISS + N_DATA = 2*68 $\endgroup$ – winni2k Jan 29 '19 at 11:11
  • 2
    $\begingroup$ My initial answer mentioned that, but that doesn't seem to hold true for all rows. Consider the following rows from their table: 22 16849476 132 0 6 0.0454545 22 16851734 126 0 36 0.285714 The N_DATA and N_MISS instead sum to 138 and 162, respectively. $\endgroup$ – spvensko Jan 29 '19 at 14:48
  • 1
    $\begingroup$ Right. That is surprising. What could cause that? $\endgroup$ – winni2k Jan 29 '19 at 15:10
  • $\begingroup$ @spvensko Great catch. My data are structural variants, maybe that is why? Thanks. $\endgroup$ – Death Metal Jan 29 '19 at 21:50

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.