> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/microarray/general/microarray-general-faq-list/000008555.md).

# What GTC files can be used with DRAGEN Array Local?

Legacy Genotype Call (GTC) files generated on scanning instruments such as the iScan or NextSeq 550, or produced by software applications such as Beeline AutoConvert or LIMS AutoCall, can be used with the DRAGEN Array Local 'genotype gtc-to-vcf' command to generate Single Nucleotide Variant (SNV) Variant Call Format (VCF) files. However, these legacy GTC files are not compatible with downstream analyses, including Cytogenetics Copy Number Variation (CNV) and Loss of Heterozygosity (LOH) calling, or pharmacogenomics (PGx) commands.

For these analyses, the use of the DRAGEN Array end-to-end workflow starting from IDAT files is recommended:

* 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.

**Reference:**

[DRAGEN Array User Guide,](https://help.dragenarray.illumina.com/) DRAGEN Array Local Analysis section.

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #8555), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000008555%20-%20Microarray%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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