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