How do you convert vcf file to a genotype file useable by eigenstrat
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4 weeks ago
RNAseqer ▴ 190

I am looking to use an R based eigenstrat function that takes " a m*n matrix, in which the element in the ith row and the jth column represents the genotype of the jth subject at the ith marker" like so:

210110202102111010121212102121
010012122220120012110202211101
011111201220222102211111101020
022120221212012102120012010112
121212001022012011111100211012
201010021010122010111112200222
100221111100021001011100221111
112012112001211001101110000211

Does anyone know if vcftools or some other package can make this conversion from a vcf file? If so do you know the command to do so?

conversion vcf format eigenstrat • 83 views
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