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Tool: Illumina BeadArray GTC to VCF conversion

An open-source utility for converting Illumina bead array GTC files to VCF format is now available at https://github.com/Illumina/GTCtoVCF. Features include

  • Indel support
  • Multi-nucleotide variant support
  • Tri-allelic loci support
  • Sites VCF generation from manifest alone

GTC is a binary format encoding genotyping information for a single sample on Illumina's bead array platform. The AutoCall and AutoConvert utilities (see https://support.illumina.com/array/downloads.html) can be used to generate GTC files. For additional information on custom processing of GTC files, see https://github.com/Illumina/BeadArrayFiles.

illumina gtc vcf beadarray
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updated by Ram Ram • written by KelleyRyanM • KelleyRyanM

1 answer

I wrote gtc2vcf, a high performing bcftools plugin to convert Illumina GTC files to VCF on Linux. It can also be made to work with IDAT files. Some features are currently missing (as of 2018-07-11) but I plan to include them in the future if there is demand.

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written by Giulio Genovese • Giulio Genovese

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