Question

How to convert CEL data to Bed/Bim/Fam/VCF for plink

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rliang1994 • 0

@rliang1994-17880

Last seen 5.5 years ago

Hi I am new to bioinformatics research and was tasked with converting (SNP array 6.0) CEL to VCF for Michigan Server Imputation. I am not quite sure how to get started as all the links/tutorials that I looked up on Google are either out of date or the link doesn't exist. Here is what my sample CEL file looks like:

3b01 0000 0001 0000 3d6d 0000 001b 6166
6679 6d65 7472 6978 2d63 616c 7669 6e2d
696e 7465 6e73 6974 7900 0000 3630 3030
3030 3237 3237 342d 3132 3437 3039 3031
3030 2d30 3030 3030 3231 3233 382d 3030
3030 3030 3737 3139 2d30 3030 3030 3030
3033 3800 0000 0000 0000 0500 6500 6e00
2d00 5500 5300 0000 2b00 0000 1900 6100
6600 6600 7900 6d00 6500 7400 7200 6900
7800 2d00 6100 6c00 6700 6f00 7200 6900
7400 6800 6d00 2d00 6e00 6100 6d00 6500

If anyone can help me regarding what R library to download or any other way to get started that would be much appreciated!

affymetrix microarrays affymetrix 6.0 • 2.1k views

ADD COMMENT • link updated 5.5 years ago by James W. MacDonald 65k • written 5.5 years ago by rliang1994 • 0

score 1 · Answer 1 · 2018-10-19

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 3 hours ago

United States

In general you would process the celfiles using the crlmm package. There are several vignettes for that package that you could read. As for converting the calls to Plink compatible format, that's something you could use the GWASTools package to do.

ADD COMMENT • link 5.5 years ago James W. MacDonald 65k

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Thanks for the answer James! Would I need to use apt-cel-convert first on the data I have above or can i just use ascii for crlmm?

ADD REPLY • link 5.5 years ago rliang1994 • 0

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An ASCII celfile should just be a bunch of numbers (text format), which wouldn't include things like 3b01, so I'm not sure you have ASCII. But regardless, crlmm uses read.celfile from the affyio package, which can read in either format.

ADD REPLY • link 5.5 years ago James W. MacDonald 65k