Question about genetic map

[Youpu-Chen]

Hi, I have a question about how to analyze the 1000 Genomes Project (hg38) dataset. I searched across the Internet, and I did not find a usable genetic map for the dataset, it always report the error below:

Is there any solution to solve this error?

[szpiech]

I've used the hg38 genetic map here: https://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/. You may need to slightly reformat it for use with selscan. I believe this map is a liftOver of a map inferred on an earlier build.

[TanXinjiang]

You can use "predictGMAP"to interpolate the loci not included in the genetic maps from the 1000 Genomes project

[Youpu-Chen]

Thank you! I've already tried predictGMAP out, but I think PLINK might just be useful enough for the analysis I've been conducting right now.

TanXinjiang @.***> 于2023年4月23日周日 16:57写道：

You can use "predictGMAP https://github.com/szpiech/predictGMAP"to interpolate the loci not included in the genetic maps from the 1000 Genomes project

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[Youpu-Chen]

I've used the hg38 genetic map here: https://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/. You may need to slightly reformat it for use with selscan. I believe this map is a liftOver of a map inferred on an earlier build.

Thank you, I also found that Eagle also provide the hg38 genetic map.