Conversation from .idat to .vcf

[Sintia Belangero]

Dear PLINK-users,

Is there any way to convert .idat to .vcf without going through Genome Studio? The only format accepted as an input file in Plink is .vcf, correct?

Thank you.

Sintia 

-----------------------------------

  Sintia I. Belangero

  Universidade Federal de São Paulo

  São Paulo-SP / Brazil

  https://www.unifesp.br

  http://pgtunifesp.com.br

[DAVID J Cutler]

Sintia,

An .idat file is an image of a chip, I believe. A lot of very specific
Illumina analysis has to be done to take an image into genotype calls,
and there is no conceivable way to do that without knowing exactly how
Illumina designed the chip, and that sort of information isn't really available
outside of illumina software.

Cheers,
dave

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[Kevin Esoh]

Hi Sintia,

Indeed, you will need the Illumina Array Analysis Platform Genotyping Command Line (iaap-cl) to process IDAT (Illumina intensity) files.
Luckily, iaap-cl is freely available here: https://emea.support.illumina.com/downloads/iaap-genotyping-cli.html
All you need is to have an Illumina account and then you can download it.

What you actually use in the iaap-cl is the Illumna gencall algorithm which will convert the IDAT files to GTC (preferably, if you wish to get a VCF at the end)
You will then use the tool gtc2vcf to generate your VCF file.

All the steps have been described on the gtc2vcf GitHub page perfectly: https://github.com/freeseek/gtc2vcf
You will notice that gtc2vcf has been ported into bcftools as a plugin, which makes it quite simple to use.
You can download the most recent version of the tools from the Broad Institute site: https://software.broadinstitute.org/software/gtc2vcf/

NB: Importantly, you will need the manifest and cluster files that are specific to the chip used to generate your IDAT files.

Here are sample codes I used to process my IDAT files after installing the tools

Convert IDAT to GTC

gencall \
   manifest/H3Africa_2017_20021485_A3.bpm \
   manifest/GenomeStudio-H3Africa-array-clusters-HapMap2-186-samples.egt \
   calls \
   --idat-folder intensities \
   --output-gtc \
   --gender-estimate-call-rate-threshold 0.95 \
   --gender-estimate-x-het-rate-threshold 0.2

intensities is the directory containing the .idat files or the subdirectories containing the .idat files

Convert GTC to VCF

bcftools +gtc2vcf \
   --bpm manifest/H3Africa_2017_20021485_A3.bpm \
   --csv manifest/H3Africa_2017_20021485_A3.csv \
   --egt clusterFile/GenomeStudio-H3Africa-array-clusters-HapMap2-186-samples.egt \
   --gtcs aw2019.gtc.list \
   --fasta-ref ~/esoh/data/db/human_g1k_v37.fasta.gz \
   --extra calls/AW2019_genotype_stats.tsv | \
   bcftools sort -T ./bcftools-sort.XXXXXX | \
   bcftools norm \
   --threads 15 \
   --no-version \
   -Oz \
   -c x \
   -f ~/esoh/data/db/human_g1k_v37.fasta.gz | \
   tee vcf/AW2019.vcf.gz | \
   bcftools index \
   --threads 15 \
   -ft \
   --output vcf/AW2019.vcf.gz.tbi

I hope this helps

Cheers,

Esoh

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--

Kevin Esoh

SADaCC Research Fellow

GeneMAP Research Center

Division of Human Genetics

University of Cape Town

Cape Town, South Africa

[Sintia Belangero]

Dave and Esoh,

It will be super useful and helpful! 

Thank you very much.

My best 

--

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  Sintia I. Belangero

  -Associate Professor, Department of Morphology and Genetics 

  -Coordinator of The Lab of Integrative Neuroscience (LINC)

  Universidade Federal de São Paulo