8000 ref-panel-map · Issue #35 · sdtemple/isweep · GitHub
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nickychapman opened this issue May 7, 2025 · 1 comment
Open

ref-panel-map #35

nickychapman opened this issue May 7, 2025 · 1 comment

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@nickychapman
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I have a question about the parameter ref-panel-map - is this file that lists the reference panel by sample and population? Is it ok if this is a subset of the reference data provided?
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sdtemple commented May 9, 2025

Yes, it is okay if the ref-panel-map file list only a subset of the samples in the reference data. In this case, all samples in the reference data will be used for phasing (Beagle), but only samples in the ref-panel-map file will be used for local ancestry inference (Flare). The ref-panel-map file is tab-separated with column 1 as Sample ID and column 2 as Reference Population Label. For an example with 1000 Genomes data, you may use all 3202 samples as your reference data GDS or VCF file, but specify in the ref-panel-map file that your references for local ancestry inference are the YRI, CEU, and CHB groups.

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