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
•
written
by
bharata1803
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
Yes, I have checked the bam file and there is no reads around that position. Now, I understand the meaning. Thank you.
Log in to answer this question.
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
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.
Please use the formatting bar (especially the
codeoption) to present your post better. I've done it for you this time.