Question: Difference between . and ./. for missing genotype in VCF
0
gravatar for William
6 months ago by
William4.4k
Europe
William4.4k wrote:

What is the difference between . and ./. for a missing genotype in a VCF file? For example in one VCF record I have these two sample genotypes.

GT:AD:DP:GQ:MMQ:PGT:PID:PL    .:0,0:.:.:.:.:.:.       ./.:0,0:0:.:.:.:.:0,0,0

There is also is a difference in which genotype attributes are 0 or .

vcf • 467 views
ADD COMMENTlink modified 6 months ago by Santosh Anand4.8k • written 6 months ago by William4.4k
3
gravatar for Santosh Anand
6 months ago by
Santosh Anand4.8k
Santosh Anand4.8k wrote:

Each DOT represents one missing allele.

. => Haploid organism

./. => Diploid organism

See VCF specs whenever in doubt http://www.internationalgenome.org/wiki/Analysis/vcf4.0/

I guess that your VCF is old (and hence doesn't follow the convention) as usually you will not find haploids and diploids in the same VCF.

ADD COMMENTlink written 6 months ago by Santosh Anand4.8k
3

Could be X chromosome, in which case males and females can be represented in the same VCF.

ADD REPLYlink written 6 months ago by Emily_Ensembl18k

The single record is from the output of a recent variant calling of a diploid organism with GATK4. GATK4 variant called multiple samples via GenotypeGVCFs (i.e. there was intermediate GVCF output that was later merged).

ADD REPLYlink modified 6 months ago • written 6 months ago by William4.4k

Oh thanks @Emily, I completely forgot about the Sex-chromosomes!

ADD REPLYlink written 6 months ago by Santosh Anand4.8k
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