VCF_format, a point in REF/ALT columns

Question

[iraun]

Hi all,

Maybe this is a basic question but I am a bit confused about vcf-format... My question is, what's the meaning of a point ".", in the REF or ALT columns? Ex.:

#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO
20     1230237 .         T      .       47   PASS   NS=3;DP=13;AA=T

Thanks in advance.

[Pierre Lindenbaum]

I can see a '.' in ID and FILTER, not in REF and ALT.

[iraun]

Oh sorry, my mistake, see my new edit.

Answer 1

[Pierre Lindenbaum]

from the SPEC: http://samtools.github.io/hts-specs/VCFv4.2.pdf

If there are no alternative alleles,then the missing value (.) should be used

(no variation was called here)

[iraun]

So, there is a line in vcf file suggesting that a variant has been found in that position, but actually there is no variant?

[DG]

Depending on how you called your variants, you may have output all positions to the VCF. This is the default (I believe) in GATK UnifiedGenotyper for instance, you have to explicitly tell it to only output variant positions.

[Vivek]

This is correct and to add, this also happens in multi sample VCFs where a locus is successfully genotyped in one sample and lacks sufficient coverage in another sample.

[bruce.moran]

Single base deletion?

[Pierre Lindenbaum]

deletion would be .eg: TA/T

[iraun]

I see, Thanks all for the explanations, now it is a little more clear. :)