How to identify Homozygous or Heterozygous variants from the annotation file ?

Question

[deepue]

Hi,

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

Thanks

[iraun]

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.

[deepue]

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

Answer 1

[Kevin Blighe]

To carry zygosity through from the VCF, you should use --withzyg with annovar/convert2annovar.pl when converting the VCF to ANNOVAR-ready format. An example is given here: http://annovar.openbioinformatics.org/en/latest/user-guide/input/#-vcf4-format

Kevin