Read binary Illumina GTC files (1000 genomes)

Question

[QVINTVS_FABIVS_MAXIMVS]

I downloaded the raw idat and gtc files from 1000 genomes

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/hd_genotype_chip/

I've worked with gtc files before; usually when I read a gtc file it's formatted like this

[Header]
Autocall Version        1.6.2.2
Processing Date xxxxxxx
Content xxxxxxx
Cluster File    xxxxxxxxx
Gender  F
Num SNPs        588454
Total SNPs      588454
Num Samples     1
Total Samples   1
[Data]
SNP Name        Chromosome      Position        GC Score        Allele1 - Top   Allele2 - Top   Allele1 - AB    Allele2 - AB    X       Y       Raw X   Raw Y   R Illumina      Theta Illumina  bAllele Freq    Log R Ratio Illumina
1KG_1_100177980 1       100177980       0.48461673      D       D       A       A       0.94567627      0.059305623     5804.0  416.0   1.0049819       0.039871734     0.004416389     -0.24513713
1KG_1_108681808 1       108681808       0.89722306      D       D       A       A       1.3823626       0.10066457      8442.0  680.0   1.4830272       0.046277393     0.0276307       -0.13262351

But when I try to read one of the gtc files in the 1000 genomes document it gives a binary file error and I cannot read it.

I tried looking up some software but I don't know what to do really?

How do I convert binary gtc files into the example I gave above?

[NS]

How do you create a manifest file required for Illumina's GTCtoVCF python source. I have the idat and gtc file but not the manifest file. Can someone please tell me how can I generate that ?

Thanks

Answer 1

[byblosopher]

Hey there - I'm having a similar issue. With GenomeStudio 2.0 I can create genotyping projects with the idat, cluster and manifest but i have no idea how to open the GTC file which should have the genotyping call data, which is all I need.

If you have you have managed to solve this, could you provide any pointers on how to open and read gtc files?

[blrhgeruser1]

Please see my answer about the open-source Python GTC file parsing library from Illumina: https://github.com/Illumina/BeadArrayFiles

Answer 2

[blrhgeruser1]

Illumina has published an open-source file parser for GTC files on GitHub: https://github.com/Illumina/BeadArrayFiles

Included are the file format specification and an example script that lets you generate final report files as you would normally do with GenomeStudio.

Answer 3

[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.

[curious]

Thank you for making this.