User: freeseek
freeseek • 100
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about me
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... You can use Illumina proprietary GenCall algorithm to generate GTC files out of IDAT file, there are now two approaches:
(i) using the Illumina Array Analysis Platform
(ii) using the Illumina Beeline/AutoConvert software
I describe how to use either approach on Linux [here][1]
[1]: https://git ...
written 12 months ago by
freeseek • 100
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... If instead of using CRLMM you are okay with using Illumina proprietary GenCall algorithm to generate GTC files out of IDAT file, there are now two approaches:
(i) using the Illumina Array Analysis Platform
(ii) using the Illumina Beeline/AutoConvert software
I describe how to use either approach ...
written 12 months ago by
freeseek • 100
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... You can use my bcftools plugin [gtc2vcf][1] as follows:
bcftools +gtc2vcf --idat file.idat
There is header information both at the beginning and the end of an IDAT file though
[1]: https://github.com/freeseek/gtc2vcf ...
written 12 months ago by
freeseek • 100
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... To recall IDAT files using Illumina proprietary GenCall algorithm there are now two approaches:
(i) using the Illumina Array Analysis Platform
(ii) using the Illumina Beeline/AutoConvert software
I describe how to use either approach on Linux [here][1]
[1]: https://github.com/freeseek/gtc2vcf ...
written 12 months ago by
freeseek • 100
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... You can also use my bcftools plugin [gtc2vcf][1] with option --idat to see the content of an IDAT file in text format
[1]: https://github.com/freeseek/gtc2vcf ...
written 12 months ago by
freeseek • 100
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... You can use my own bcftools plugin [gtc2vcf][1] to convert GTC files to VCF
Then it is easy to convert a VCF file to PLINK format using [best practices][2]
[1]: https://github.com/freeseek/gtc2vcf
[2]: http://apol1.blogspot.com/2014/11/best-practice-for-converting-vcf-files.html ...
written 12 months ago by
freeseek • 100
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... 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 bc ...
written 12 months ago by
freeseek • 100
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... I wrote affy2vcf, a bcftools plugin that is capable of generating VCF files out of the output of the Affymetrix apt-probeset-genotype command line tool. ...
written 2.4 years ago by
freeseek • 100
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... 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. ...
written 2.5 years ago by
freeseek • 100
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... 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. ...
written 2.5 years ago by
freeseek • 100
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