How to create manifest file for Illumnina GTCtoVCF

Question

[NS]

Hi

I have several idat and gtc files. I want to convert them to standard vcf format to obtain the genotype information. I found that llumnia has developed a python source for parsing gtc files (https://github.com/Illumina/GTCtoVCF). However it requires manifest file / Bead pool manifest.

So my question is :
1) How can I create a manifest file using idat or gtc files that I have ?
2) What is the format of the manifest file, what information does it contain ?

Thanks

Answer 1

[Giulio Genovese]

1) You cannot create a manifest file from IDAT or GTC files

2) A manifest file contains information about the location of the probes in a genotyping array and it is required both to convert IDAT files to GTC files using GenCall and to interpret genotype calls out of GTC files

You can use my own bcftools plugin gtc2vcf which is a much more efficient version than the GTCtoVCF software to convert GTC files to VCF

Illumina provides manifest files for most of its arrays and you can also use my plugin to update coordinates to GRCh38 during the conversion to VCF