Question: 1/2 in VCF genotype field?
gravatar for mbk0asis
2.8 years ago by
Korea, Republic Of
mbk0asis410 wrote:


I made vcf files using UnifiedGenotyper in GATK and found that many of mutants had 1/2 at genotype (GT) field.

As I understand, 0/0 = homo ref, 0/1 = hetero, 1/1 = homo alt.

Does anyone know what exactly 1/2 mean?

Thank you!

zygosity vcf • 2.2k views
ADD COMMENTlink modified 2.8 years ago by Jorge Amigo11k • written 2.8 years ago by mbk0asis410
gravatar for Jorge Amigo
2.8 years ago by
Jorge Amigo11k
Santiago de Compostela, Spain
Jorge Amigo11k wrote:

just to expand Devon's answer, which is perfectly correct...

this is due to a VCF format constrain, which states that 0 must always be the reference allele. this doesn't mean that the reference allele must be in a particular sample, it just means that a particular base is used as reference by a scientific community agreement.

in case you're working with human samples, this agreement is now supported by the Genome Reference Consortium, and I really hope that when the time comes (we shouldn't be that far) they'll be able to build a consensus reference based on entire world populations allele frequencies, but meanwhile we have to stick to the current reference. current GRCh38 has already done some work in this direction though.

since humans are diploids, sequencing a particular position will give you a pair of alleles, and usually the reference will be 1 of that 2 alleles. but this is not always the case, and you may find (as you already did) that a particular position doesn't contain the reference allele. this is rare, but far from being impossible due to the lack of population genetics evidences in the reference selected, as explained previously.

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Jorge Amigo11k
gravatar for Devon Ryan
2.8 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

There are apparently two alternate alleles at this position. So if the reference is C, then perhaps you have an A and a G.

ADD COMMENTlink written 2.8 years ago by Devon Ryan88k
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