Question: How to identify Homozygous or Heterozygous variants from the annotation file ?
gravatar for deepue
5.2 years ago by
deepue130 wrote:


I am new to the NGS analysis and wondering how one can identify whether a variant is a Homozygous or Heterozygous from the annotated file? If yes, How to play with the columns in the annotated file ?

I could see that this can be interpreted from the vcf file like below (source this post).

GT : The genotype of this sample. For a diploid organism, the GT field indicates the two alleles carried by the sample, encoded by a 0 for the REF allele, 1 for the first ALT allele, 2 for the second ALT allele, etc. When there's a single ALT allele (by far the more common case), GT will be either:

  • 0/0 - the sample is homozygous reference
  • 0/1 - the sample is heterozygous, carrying 1 copy of each of the REF and ALT alleles
  • 1/1 - the sample is homozygous alternate


snp next-gen • 14k views
ADD COMMENTlink modified 23 months ago by Kevin Blighe63k • written 5.2 years ago by deepue130

There are different ways to know the genotype of a given variant. GT field is probably the best one to use, but there are another fields of interest to know the genotype as AF (Allele Frequency). In order to extract homo or hetero variants, there are different tools like: GATK SelectVariants, SnpSift ...etc.

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by iraun3.8k

I am interested to know these details from the annotated annovar file.

ADD REPLYlink written 5.2 years ago by deepue130
gravatar for Kevin Blighe
23 months ago by
Kevin Blighe63k
Kevin Blighe63k wrote:

To carry zygosity through from the VCF, you should use --withzyg with annovar/ when converting the VCF to ANNOVAR-ready format. An example is given here:


ADD COMMENTlink written 23 months ago by Kevin Blighe63k
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