Hello,
I am in the process of creating a merged reference panel which will
include 250 WGS samples from an isolated population. I wish to merge these
with the latest 1000 genomes that has already been merged with ~4,000 UK
WGS samples. I will use this 3-way merged reference for the imputation of
the rest of the isolated cohort.
I have noticed that there are ~10,000 variants that have different alleles
in the 250 WGS isolated population compared to the other two reference
panels. My question is can I keep both variants in or will this cause
problems for me later?
I assume I will end up with duplicates which I will deal with by perhaps
modifying the SNP id so that I can tell where it originates from. I am
loath to discard these SNPs from my 250 WGS samples as these variants have
passed all of our QC filters and may be real and important in this
population.
Any advice greatly appreciated,
Loz
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