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Add support for PACKEDANCESTRYMAP format #303

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TCLamnidis opened this issue Jun 25, 2024 · 2 comments
Open

Add support for PACKEDANCESTRYMAP format #303

TCLamnidis opened this issue Jun 25, 2024 · 2 comments
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enhancement New feature or request

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@TCLamnidis
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It would be great to add support for PACKAEDANCESTRYMAP format. It is the binary EIGENSTRAT format, and is used internally by some tools to speed up computations (qpWave/Adm/Graph run WAY faster when the input is in this format).

It makes a lot of sense to support this format in poseidon imo, as an option for trident genoconvert.

@TCLamnidis TCLamnidis added the enhancement New feature or request label Jun 25, 2024
@nevrome
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nevrome commented Jun 28, 2024

In the past @stschiff has argued against support for formats beyond EIGENSTRAT, PLINK and VCF: #150

But maybe a concrete usecase and our plan to finally add support both for VCF (poseidon-framework/poseidon-schema#45) and for compressed archives (#237), which requires an overhaul of the genotype reading functionality anyway, may help to sway his mind?

@stschiff
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stschiff commented Jul 2, 2024

I would have to take a look. My reservations are:

  • All of these formats, including Eigenstrat and Plink are somewhat outdated and poorly specified (see also reviewers' comments of our paper)
  • As far as I know it's a single, albeit widely used, software suite that requires these formats. What about ADMIXTOOLS2? Has that superseded the need for those to some extent?

It is of course in principle easy enough to add support for more file formats, though.

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