Question

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

1

Entering edit mode

9.9 years ago

m338102001 ▴ 10

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 • 5.0k views

ADD COMMENT • link updated 2.5 years ago by Ram 43k • written 9.9 years ago by m338102001 ▴ 10

Ram · Answer 1 · 2015-03-19

1

Entering edit mode

9.2 years ago

andrew.mcpherson ▴ 10

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

ADD COMMENT • link updated 2.5 years ago by Ram 43k • written 9.2 years ago by andrew.mcpherson ▴ 10

Ram · Answer 2 · 2014-07-04

0

Entering edit mode

9.9 years ago

chrchang523 10k

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.

ADD COMMENT • link updated 2.5 years ago by Ram 43k • written 9.9 years ago by chrchang523 10k

Ram · Answer 3 · 2014-07-07

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?