Dear all,
Apologies for sending around the same question, I didn't have any response
but I have had a few enquiries from people asking if I had a response to
the message I posted so I know that there are others out there interested
in this.
For this reason I am asking for help again! I wonder if anyone has any
experience doing this or can offer advice.
Best wishes,
Loz
On Mon, November 11, 2013 4:58 pm, [log in to unmask] wrote:
> 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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