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

Question

[tarek.mohamed]

​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

[h.mon]

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

[tarek.mohamed]

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

[h.mon]

Check for pointers on Recalling SNPs count from Illumina SNP array raw data, Read binary Illumina GTC files (1000 genomes) and Illumina HumanOmniExpress IDAT files.

Answer 1

[Giulio Genovese]

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.