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