haploid imputation of parental haplotypes
Table of contents
That’s it, you are at the end of our parent-of-origin inference tutorial.
The previous step allowed you to produce three files:
${output}.paternal\_haplotype.vcf.gz${output}.maternal\_haplotype.vcf.gz${output}.differential\_haplotype.vcf.gz
If you wish to run association testing, using for example REGENIE, you can simply convert these file to .bgen or .pgen format using plink2 for example.
In our parent-of-origin effects analysis, we typically used the “differential” haplotype to obain what we refer to as a POE p-value and identify parent-of-origin effects. In addition, we also typically run a GWAS for the paternal haplotype and for the maternal haplotype, which allows us to classify the POEs into maternal effect, paternal effect, bi-polar effect, or a more complex POE pattern.
For any question on this tutorial, you can contact Robin Hofmeister at robin.j.hofmeister@gmail.com or robin.hofmeister@unil.ch