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Old 03-22-2012, 10:52 AM   #1
ElMichael
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Default Dataset (PLINK format): conversion from b36 to b37

Hi,

I have a dataset in the binary PLINK format from the Illumina 1M array. Samples were genotyped on the array, designed to human genome build 36. But now I need to convert it to b37. What is the best way to do it? I read about some Illumina conversion files but didn't find them.

Thanks!
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Old 03-22-2012, 03:02 PM   #2
turnersd
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liftOver the map file.

http://hgdownload.cse.ucsc.edu/downloads.html
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Old 03-22-2012, 03:51 PM   #3
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But what is about those snps whose position was changed even to another chromosome? And snps whose rs ID was changed?
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Old 03-22-2012, 04:01 PM   #4
turnersd
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I think the liftover would fix the chromosome issue (probably, others? comments?) but not sure about the rs ID mapping.
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Old 03-23-2012, 08:59 AM   #5
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Thank you, turnersd!
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