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.