Question: Change rsID to chromosome:location in bim files for plink
1
gravatar for amitgourav.ghosh12
12 months ago by
amitgourav.ghosh1260 wrote:

Some of the SNPs in my dataset are without rs ids, so in the bim file, they have dots instead of rs ids for them. So for errorless analysis how should replace the rs id column with that of the chromosome: location column instead?

snp plink genome • 1.0k views
ADD COMMENTlink modified 12 months ago by chrchang5236.9k • written 12 months ago by amitgourav.ghosh1260
3
gravatar for chrchang523
12 months ago by
chrchang5236.9k
United States
chrchang5236.9k wrote:

This can also be done with plink 2.0's --set-all-var-ids flag.

But it's more valuable to understand the awk solution, since that opens the door to a broadly useful set of text-manipulation techniques.

ADD COMMENTlink modified 12 months ago by zx87549.2k • written 12 months ago by chrchang5236.9k
2
gravatar for zx8754
12 months ago by
zx87549.2k
London
zx87549.2k wrote:

Using awk, (not tested):

awk '{if($2 == ".") {print $1,$1"_"$3,$4,$5,$6} else {print $0}}' myfile.bim > myfileClean.bim
ADD COMMENTlink written 12 months ago by zx87549.2k
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