This is a test version of Biostars. For the public version, visit https://www.biostars.org.
VCF_format, a point in REF/ALT columns

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.

vcf-format
• 8,169 views • link
updated by Ram Ram • written by iraun iraun

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

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Oh sorry, my mistake, see my new edit.

• 0 views • link
written by iraun iraun

2 answers

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)

• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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

• 0 views • link
written by iraun iraun

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

• 0 views • link
written by iraun iraun

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.

• 0 views • link
written by DG DG

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.

• 0 views • link
written by Vivek Vivek

Hi,

I am using COSMIC vcf file to make hotspot bed file but in ALT column of COSMIC vcf contains N & . characters so software I am using ignores that COSMIC ID while making hotspot bed file. It will be great if anybody could help me.

Thanks in advance.

• 0 views • link
updated by Ram Ram • written by vdtbioinfo • vdtbioinfo

You should probably create a separate post for you question otherwise people won't find your question and won't be able to answer.

• 0 views • link
written by Lesley Sitter Lesley Sitter

Log in to answer this question.

More posts like this