What is the input to Plink's distance matrix function?
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21 months ago

I want to calculate a pairwise distance matrix (DM) on several samples (~100). When I look at Plink's documentation for calculating a DM, at no point does it seem to give a clue as to what the input file has to be. https://www.cog-genomics.org/plink/1.9/distance.

Am I missing something really obvious here?

I have a concatenated vcf for these samples. Will this suffice?

Thanks

plink dist distance matrix • 841 views
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What do you mean by concatenated VCF? If you've called the variants from multiple samples in a single vcf file i.e. every sample is a column after the INFO columns, that should be enough. If not you need to use bcftools merge to merge your vcf files.

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