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GATK: how to change vcf.gz file into genotype matrix

I am quite new about vcf.gz file. Can some tell me how to change vcf.gz file into genotype matrix with value 0,1,2?

vcftools gatk

I tried here. But I have problem, that is the length of chr.012.pos is not same as the length of rows of chr.012

Hello zwang10!

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