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How to extract raw genotype calls from idat or gtc illumina files

​Hi folks,

I used the cytosnp-12 bead chip for karyotyping of some samples. I have the idat and gtc files which I analysed using bluefuse multi software. Now I need to get the raw genotype calls, how can I extract this data?

Thanks, Tarek

gtc files idat files raw genotype calls
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updated by Giulio Genovese • Giulio Genovese • written by tarek.mohamed tarek.mohamed

What is the output of BlueFuse Multi? Extract raw calls from idat or gtc? Or extract from downstream files?

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written by h.mon h.mon

Hi, I have both files, so I want to extract raw genotype calls from either of them. Thanks, T

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written by tarek.mohamed tarek.mohamed

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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