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Reorienting 1000 Genome VCF files, so that derived alleles are always ALT
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18 months ago
devenvyas • 570
Stony Brook


I am working with the 1000 Genomes Project phase 3 VCF files. I am trying to figure out how to reorient the REF and ALT alleles so that the derived allele is always the ALT.

I tried the --derived option in vcftools, but that apparently does nothing for the VCF output files.

vcf snp • 111 views

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