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how to deal with snps with different name but same bp pos in plink map file?

dear everyone,

I'm handling a plink file and preparing to use SHAPEIT to do phasing.

But the software come out with an ERROR: duplicate site pos=1263163, and after grepping the pos in map file, I found out that:

2     exm169593 0 1263163
2     rs140313765 0 1263163

after checking, I also found that there are many snps with the same condition. so I want to remove the exm one from the map file, but I have no idea how to deal with it.

Please give me some suggestions and thanks for your kindly help.

henry :D

snp shapeit
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updated by Ram Ram • written by m338102001 • m338102001

3 answers

Use the --exclude-snp option to remove the duplicated snps from the analysis.

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updated by Ram Ram • written by andrew.mcpherson • andrew.mcpherson

What program generated this error? I'd expect PLINK and SHAPEIT to have no problem with this; it's common in e.g. 1000 Genomes data.

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updated by Ram Ram • written by chrchang523 chrchang523

I believe he used SHAPEIT, I get the same error from an gen-file I'm trying to phase.

One work-around I think may work is converting it to a ped/map file using gtools and then converting this to a bed-file using plink and finally phase that bed-file using SHAPEIT.

I have not tried this personally, but will in a moment.

EDIT: I tried it, and my thought that it would clean/merge did not work out. I get the same error. If the number of sites are negligible - delete one of them?

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updated by Ram Ram • written by okrantz • okrantz

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