What GTC files can be used with DRAGEN Array Local?

DRAGEN Array Local can be used to generate Genotype Call (GTC) files, which are then used to generate SNV VCF and CNV VCF files.

• The 'genotype call' command is used to call genotypes and generate GTC files

• The 'genotype gtc-to-vcf' command is used to generate SNV VCF files

• The 'copy-number call' command is used to generate CNV VCF files

Note: The scanning instrument (iScan or NextSeq 550) or software such as Beeline AutoConvert or LIMS AutoCall also produce GTC files. These legacy GTC files will work in DRAGEN Array command 'genotype gtc-to-vcf' but are not compatible with downstream analyses such as Cytogenetics CNV and LOH calling and PGx commands. It is recommended to use DRAGEN Array end-to-end starting from IDATs for these analyses.

For more information, see the DRAGEN Array User Guide.

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