Optimal way to store genetic data (for merging, PCA plotting)?

09 July 2019 1 3K Report

There are different formats for genetic data:

VCF
PLINK (map+ped or bim+bed+fam)
EIGENSTRAT

Let we have 100 datasets with 500K SNPs (7-8M after imputation) and 1000 individuals in each dataset. For each dataset it could be its own set of SNPs.

What is the optimal format to store such data? What is the fastest tool to merge them and produce PCA plots?

Alexander Rakitko

Bharati Jadhav

thank you for the answer!

I have to store the phased genotypes so PLINK format doesn't work for me (or there are any extensions?)

VCF is a good format but it takes a lot of time to merge datasets...

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