plink2 merge

[Michael Harris]

Hi Chis,

Do you have any plans to implement merge with non-overlapping samples?  Bcftools merge can be quite slow when merging large numbers of individual VCF files.  

We are sequencing bacterial genomes and I was hoping to use plink 2 to merge around 30,000 individual VCF files into one merged multi-sample VCF.   

I would appreciate any advice that you have.  Plink2 performance and functionality  has been amazing for analyzing our samples. Thanks for providing this fantastic tool to the community!

Michael 

[Christopher Chang]

If the non-overlapping samples have exactly the same variants in the same order, and they're all biallelic, you can use the script I posted at https://groups.google.com/g/plink2-users/c/IdG7d4oSehI/m/9TQhKVDxBQAJ .

[Michael]

Thanks this is helpful!  Do you think this strategy could be used on a compute cluster with multiple nodes doing part parts of the merge with subsets of the samples  and then having a single node do the final merge of the smaller merged files ?

Thanks!

Michael