Hello,
This is a pretty basic question, yet I am unable to get clarity from the documentations of these respective softwares. I have a large number of trios (±30000) and have phased them using SHAPEIT2 + BEAGLEv4 in a pedigree aware fashion, taken care of any mendelian errors and also performed kinship studies to ensure there is no confusion for paternity.
Now getting to my question:
I have phased VCFs but am unable to interpret whether the first allele in the proband is fathers and second is mum's i.e., are they reported as "paternal | materal", or are they just the likely Haplotypes and do not correlate back to the parents?
I have manually looked at the Haplotypes for some of the trios and it does look like it is father|mother but I cannot do so for 30,000 of these families. Anyone with a clear confirmed answer on whether SHAPEIT2 and BEAGLE4 output them in a specific father|mother or random order, please do reply.
Due to crossing over during meioses, an individual inherits chunks of DNA from each parent rather than entire chromosomes. Therefore, you can’t say whether the the maternal or paternal allle always comes first. You’d have to write some kind of program to check for allele matching between proband and parent.
Thank you. I am only testing a very small region (50-100kb) and am only specifically interested in the parental origin of one variant, and am using the ones around it to check if it is paternally or maternally inherited. I did read in some places that in the presence of trio data, softwares are able to assign father/mother status to the proband's alleles if family relationships are provided. I am unclear on how I could write a program to do this for all 10,000 families as they will have different sets of heterozygous SNPs around my variant of interest, especially if they are rare. Would you have any insight into this? I would be grateful!