Few SNPs after merging my samples with 1000G phase 3
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5.9 years ago
Phoenix Mu ▴ 100

I used pruned SNPs from 1000G phase 3 to do a PCA, and got the following results: enter image description here In the plot above, different populations were well seperated, and individuals from the same population clustered tightly. ~ 20,000 SNP were used.

I then merge 1000G data with data from my study population, and PCA results looked like: enter image description here This figure is generally right. But, the points are quite scattered, and individuals from different ancestries is overlaping. I think this is because the number of SNPs used in PCA is not sufficient. Indeed, I only have ~ 900 SNPs after merging my data set with 1000G SNPs. Notably, my data also has about 20,000 SNPs before merging.

So I am wondering why there is so few SNPs after merging 2 datasets, and how to deal with it?

Thanks!

1000G pca SNP • 2.4k views
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How did you merge the datasets? Please be as complete as possible when asking questions and include commands used.

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I merged it with mergeit to in EIGENSTRAT. The tool merge two sets by finding the union of individuals and intersect of SNPs.

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Is your data from a microarray?; if 'yes', then which one? Did you perform any LD pruning?

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Actually, I have WGS data. I read a Nature Protocols article on GWAS QC and realized that I should use the complete SNPs from reference panel (1000G) to merge with my data first, and then extract SNPs from LD pruning that was done in my sample. However, I did LD pruning for both 1000G and my own data set, and this might be why there were so few SNPs after merging. Thanks!

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Yes, the part where LD pruning is performed is key, i.e., before or after merge. Best of luck!

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