VCF file period symbol in the genotype

Question

[bharata1803]

I have VCF file below:

CHROM   POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  19  21  23  25  27  29  31  33

1   69511   .   A   G   57  .   DP=36;VDB=0.341447;SGB=12.2915;RPB=0.903226;MQB=0;MQSB=0.23855;BQB=0.0645161;MQ0F=0.638889;ICB=0.0439024;HOB=0.02;AC=9;AN=10;DP4=2,0,14,17;MQ=2 GT:PL   ./.:0,0,0   ./.:0,0,0   1/1:20,18,0 ./.:0,0,0   1/1:27,24,0 1/1:21,24,0 0/1:0,6,27  1/1:30,27,0

I want to interpret the variation for each sample (19,21,23,...,33) but I noticed there are sample that have no 0/0 or 0/1, or 1/1 symbol instead ./.. What is the meaning of ./.? I tried to read the VCF file version 4.2 and there is no explanation. Thank you

[always_learning]

Hi

what could be reason of "." as genotype for Human GATK generated VCF ? i know that "./." is for missing but I am not able to understand "." for few location.

Can anyone help on this?

Thanks

[Ram]

Do not add an answer unless you're answering the top level question. In your case, you should be opening a new question and referencing this post there.

[Ram]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Answer 1

[finswimmer]

Hello,

a period in a vcf file always means "no Data" or "unknown". So in your case at these sites the genotype for samples with ./. could not be determined.

So you maybe take a look at the bam files why the variant calling failes here. Maybe the coverage is to low?

fin swimmer

[bharata1803]

Yes, I have checked the bam file and there is no reads around that position. Now, I understand the meaning. Thank you.