Question

How To Convert Illumina/Affy Array Data To Vcf Format

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10.6 years ago

sheausean • 0

Hi,

Has anyone share how can I convert Illumina/affy array data to vcf format?

Many thanks.

array data vcf format • 6.5k views

ADD COMMENT • link updated 5.6 years ago by Giulio Genovese ▴ 390 • written 10.6 years ago by sheausean • 0

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Have you not even bothered to search pubmed for papers using arrays for SNP calling to see how they did it (hint, there are bioconductor packages)?

ADD REPLY • link 10.6 years ago by Devon Ryan 104k

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I'm also trying for the same thing. Can you please tell me about those R packages?

ADD REPLY • link 5.3 years ago by Susmita Mandal ▴ 110

score 3 · Answer 1 · 2018-09-07

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5.6 years ago

Giulio Genovese ▴ 390

I wrote affy2vcf, a bcftools plugin that is capable of generating VCF files out of the output of the Affymetrix apt-probeset-genotype command line tool.

ADD COMMENT • link 5.6 years ago by Giulio Genovese ▴ 390