Merge multicore

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Paolo Di Domenico

Jun 16, 2019, 1:50:24 PM6/16/19
to plink2-dev
Is there any known way of using plink to merge binary bed files using a multithread function?
For what I know the merge function on plink2 is still on its way and this function in plink 1.9 don't use multicore.
Do you know if plink2 will use multithread in order to merge file?
There's another way to accomplish this task?
Thank you.

Christopher Chang

Jun 16, 2019, 8:57:51 PM6/16/19
to plink2-dev
Hi Paolo,

The plink2 merger will definitely use more than 1 thread, but it also has to deal with a much more general problem (phase, dosage, multiallelic variants), so I don't expect the speedup relative to plink 1.9 to be *that* large, but we'll see.

Meanwhile, what is your use case?  Are you just "concatenating" a bunch of plink filesets, where the samples are the same and only the variant IDs differ (or vice versa, the variant IDs are the same and the sample IDs differ), or do you need to do something more complicated?  Concatenation is likely to be implemented in plink 2.0 soon.
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