Question: Merging WGS SNP array data
gravatar for sankar2004
10 days ago by
sankar200410 wrote:


I combined SNP array and WGS data and plotted a PCA. I found that the individuals from the same population did not cluster together because the SNVs were obtained from the two different (genotyping) methods mentioned above. How do you remove this bias/discrepancy from these datasets.

Thanks for your help

snp • 69 views
ADD COMMENTlink modified 9 days ago by RamRS17k • written 10 days ago by sankar200410

Thanks a lot Kevin. I will try that

ADD REPLYlink written 9 days ago by sankar200410
gravatar for Kevin Blighe
10 days ago by
Kevin Blighe28k
USA / Europe / Brazil
Kevin Blighe28k wrote:

With your array data, you will have to filter out variants not called on the coding (+ / plus) strand, and then also filter these out of the NGS WGS data. Take a look at what I have written for Step 6, here: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2

You can download the library files from the array manufacturer for the purposes of determining on which strand each probe genotypes.


ADD COMMENTlink written 10 days ago by Kevin Blighe28k
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