We are dealing with relatively large family data (> 1,000 trios) with genotyping array data. We would like to see the allele effects on children separately of mothers, fathers, and children, as in a previous study (PMID: 34282336). Unfortunately, this is difficult for us to replicate, so we need another method. Is there any software that can achieve this or a similar traditional approach? Also, can that be applied to grandparents?
In my understanding of the above mentioned study is they:
- identified the parental genomes within the child genome;
- thereon conducted a GWAS for birth weight
Overall, the aim of the previous study was to estimate the alleles responsible for birth weight or in our situation a comparable phenotype. It is important to note the prior study did not use publicly available algorithms.
Thus, we wish to identify the maternal and paternal alleles within their progeny via public domain algorithms, and therefore do not necessarily need to exactly reproduce the previous study.
We already have imputed data, and are using GCTA for usual GWAS. To achieve our goal, we need to identify the transmitted and non-transmitted alleles in parents.