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Converting Illumina to Plink

hello there

I am new to the world of genetics:), I had a question: Do genotype companies like Illumina provide PLINK-friendly files, or do we convert them?

plink
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written by Shalini • Shalini

Hello Shalini, What array data you have? and how are you analyzing the data? using genome studio ?

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written by 1769mkc 1769mkc

Thank you so much for replying at this stage I ’m trying to understand the typical workflow: whether genotyping cores usually export PLINK‑ready files (PED/MAP or BED/BIM/FAM) directly from GenomeStudio using the PLINK report plug‑in, or whether people generally export FinalReports and then convert those to PLINK themselves with scripts/tools. Any advice or best‑practice pointers would be very helpful.

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written by Shalini • Shalini

You should directly check with the provider you are planning to work with. There would likely be a basic deliverable package of results that would be included in base price. Additional analysis may be available in any format you need/want for an added cost.

When you compare prices take the additional work that may be needed into account. Especially if you don't want to or don't have the resources to do the analysis yourself.

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written by GenoMax GenoMax

Makes sense, thank you, I really appreciate your suggestion.

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written by Shalini • Shalini

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