Is haplotype phasing essential after variant calling?

Question

[seta]

Hi everybody,

Sorry if you find the question is basic for you. I want to determine variants of human blood groups genes from whole genome sequencing data of a given population. I read some about the haplotype phasing, but I'm not sure if it is essential after variant calling in my work? Could you please kindly tell me if haplotype phasing is required and why?

Thanks

Answer 1

[WouterDeCoster]

Sorry if you find the question is basic for you.

There is absolutely no need for apologies like this ;-)

I want to determine variants of human blood groups

This isn't entirely clear to me, so I'll answer more generally.

Phasing means figuring out if a variant is from the paternal or maternal haplotype. It can be important. Imagine the following scenario, in which you have two SNPs A and B in a protein X. Either A and B are on the same allele/haplotype and you have 50% "normal" and 50% "mutant" protein X with SNPs A and B. Alternatively A and B are on a different allele/haplotype (a situation called compound heterozygous) and you have two "mutant" protein X types, 50% of protein X with SNP A and 50% of protein X with SNP B.

Note that this "50%" is theoretical, in biology it will never be exactly 50-50

So these both scenarios can have vastly different outcomes, biologically.

[seta]

Thank you very much for your nice explanation. The initial variant analysis showed that there is the high rate of variation in our data (that is from a given population) in comparison to the human reference genome, so reference genome or HapMap cannot be used for haplotype phasing, yes? Could you please let me know your solution in this situation? If you suggest making a reference panel, please kindly advise me the appropriate tools/pipelines for starting point.

Many thanks