User: freeseek

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freeseek100
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Posts by freeseek

<prev • 24 results • page 2 of 3 • next >
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Answer: A: Are there any GenomeStudio alternatives to process Illumina genotyping array?
... 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 freeseek100
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Answer: A: From genotype raw data .idat to PLINK files
... 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 freeseek100
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Answer: A: How to extract and save the header of .bam,vcf and idat files in a text file
... 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 freeseek100
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Answer: A: Recalling SNPs count from Illumina SNP array raw data
... 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 freeseek100
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Answer: A: how to use idat file for analyses in bioconductor
... 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 freeseek100
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Answer: A: genotyping according to the red/green intensity for illumina microarray?
... 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 freeseek100
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Answer: A: How to create manifest file for Illumnina GTCtoVCF
... 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 freeseek100
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Answer: A: How To Convert Illumina/Affy Array Data To Vcf Format
... 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 freeseek100
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Answer: A: Illumina BeadArray GTC to VCF conversion
... 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 freeseek100
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Answer: A: How to extract raw genotype calls from idat or gtc illumina files
... 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 freeseek100

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