Question: How to identify Homozygous or Heterozygous variants from the annotation file ?
gravatar for deepue
3.9 years ago by
deepue110 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 • 10k views
ADD COMMENTlink modified 7 months ago by Kevin Blighe41k • written 3.9 years ago by deepue110

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 3.9 years ago • written 3.9 years ago by iraun3.5k

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

ADD REPLYlink written 3.9 years ago by deepue110
gravatar for Kevin Blighe
7 months ago by
Kevin Blighe41k
Kevin Blighe41k 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 7 months ago by Kevin Blighe41k
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