What is the best software for "phasing" in human population genomics with trio family pedigree?

Question

[Daniel]

Hi,

I am new to bioinformatics. Currently I have the a list of identified SNPs from trio human population. I am planning to do phasing to figure out the proportion of the SNPs coming from paternal and maternal? I also have the pedigree file as well.

Just wondering what is the best R package, software that help me to do such analysis? Dose SHAPEIT4 or smartphase or PULSAR good for this purpose?

Answer 1

[colindaven]

If you're looking at read-backed phasing, I believe whatshap is one of the best choices (not in R AFAIK).

https://www.biorxiv.org/content/10.1101/085050v2.full.pdf

Answer 2

[curious]

beagle does it, but i think only v 3 or 4 not the most current one (v5)