Understanding haplotype notations (output from EAGLE2)

Question

[mikothebichon]

This is probably a really stupid question, but I am having some difficulty understanding the output VCF from EAGLE2. In the genotype column, I suppose "0|1" and "0|1" just mean that the REF and ALT alleles are from either parent. But what does it mean when we have "0|0" and "1|1". Does this imply the SNPs are homozygous in these positions?

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  SAMPLE_1    SAMPLE_2    SAMPLE_3    SAMPLE_4    SAMPLE_5
1       534192  .       C       T       141.89  .       AN=10;AC=3      GT      1|0     0|0     0|0     1|1     0|0
1       592007  .       G       A       873.17  .       AN=10;AC=8      GT      1|1     1|1     0|0     1|1     1|1

Answer 1

[sbstevenlee]

Yes, 0|0 means REF homozygous and 1|1 means ALT homozygous. Note that homozygous loci don't need haplotype phasing since they are already phased; however, we still use 0|0 and 1|1 to be consistent with the notation used for heterozygous loci (i.e. 0|1 and 1|0).

[mikothebichon]

Understood, thank you!