IDAT to FASTA workflow

Question

[sabrilo171]

I'm currently working in a primary GWAS from 334 samples that were sequenced with Illumina HumanCoreExome 12.1 Chips, for which I already have the IDAT files. I was able to decode them using GenomeStudio and export them as PLINK FILES (PED, MAP). I need to know how to convert those IDAT files, to FASTA or FASTQ files that could be uploaded to consortium databases for publication purposes.

I have beginner level skills in Unix/Conda, beginner level knowledge in bioinformatics, and know how to work my way with R. Considering this, it would be optimal if someone here could provide me a very clear and straightforward method (workflow) to achieve what I'm looking for.

Thank you in advance!

Answer 1

[Giulio Genovese]

An IDAT file is a raw Illumina file containing raw intensities for predetermined probes designed around known polymorphic sites. It does not contain sequence data. It should probably be okay to upload as is. These files can be processed with BCFtools/idat2gtc and then converted to VCF with BCFtools/gtc2vcf if needed. You don't need GenomeStudio to process IDAT files

[sabrilo171]

Thank you very much Dr. Genovese! Perhaps a silly follow-up question but, are IDAT files required to be uploaded to consortia in the same way as FASTA files in order to publish GWAS results? If they are, is there a specific site to do so in the NCBI website?

[GenoMax]

NCBI GEO: https://www.ncbi.nlm.nih.gov/geo/info/geo_illu.html