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PLINK to Bayescan
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2.8 years ago
Earendil • 20

I got used to handling vcf files for the most part of my work, converting them to Bayescan format with PGDSpider but now I have to deal with the plink bed/bim/fam format which I should convert to Bayescan to do my analysis. It seems that the right way to do this is to convert the files to PED plink format and then again use PGDSpider to make the Bayescan format file.

I want to make sure that there isn't any important information getting lost by the file conversion: To my understanding, the plink format files do not clearly state the reference allele but I wouldn't need that for Bayescan since we are only dealing with alleles that are observed or not and thus, the conversion would not lead to a problem.

Is the above thought correct?


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