Genomic Sequence Data: Answers to My Questions

[alexepascual]

I wonder. If I received the data (I don't know in what format) of all or part of my genome sequence, whould all the genes and SNP's that are physically in the same chromosome (not its homologous one) show together in the data or the process of sequencing and assembly mixes them up? I understand DNA is chopped in small pieces to do the sequencing. That's why I wonder if there is a way to make sure that all the small pieces that came form one of the two homologuous chromosomes (form the father or the mother) stay together. For example if two genetic variants (I mean of two different genes) show in the same chromosome, can I be sure these two came both from the same parent? I have not received yet any data, but my wife got a small set of SNP's with the intent to get some info about her ancestry. Looking at the raw data, I see that they show the SNP's from the homologous chromosomes as Allele 1 and Allele 2, and all the allele 1's are in the first column and the allele 2's are in the second column. So my question also applies to that situation. I wonder if all the allele 1's form a particular chormosome number come from the same parent or not necessarily. I would guess that maybe in that case, if we are looking at isolated SNP's it may be very hard to know which of the two chormosomes a particular allele came from. If you know about this I'll appreciate your answer.

 

[Ygggdrasil]

Determining which alleles are linked to the same chromosome is a process called haplotyping. Standard whole genome sequencing methods do not allow one to determine the haplotype of an individual. Specialized techniques, such as phased sequencing using longer read lengths and higher coverage, are required to determine one's haplotype.