How to change my SNP Id format from chr1_847228_C_T to chr1_847228 in my .bim file.

Question

[geno89]

My .bim file has format of SNP ID as chr1_847228_C_T and i want to change it to chr1_847228 format. The reason to do is i want to apply --update name flag to update my SNP ids into rs ID and the reference file have the SNP id format as chr1_847228 .

Answer 1

[Sam]

awk '{split($2,a,"_"); print $1,a[1]"_"a[2],$3,$4,$5,$6}' bim > new_bim

might work. This will "tokenize" your rs_id by _ and then make a new id by combining the first and second item together.

[geno89]

Hi. Thanks it worked well to remove allele from chr1_847228_C_T but as my SNP ID column contains some other formats too like rs2880024 and exm888888 so it changed them to rs2880024_ and exm888888_. How can i remove this "_" from them. Thanks

[Sam]

Then you can do awk '{n=split($2,a,"_"); if(n>=2){print $1,a[1]"_"a[2],$3,$4,$5,$6}}else{print $1,$2,$3,$4,$5,$6}' bim > new_bim

You can also do print $0 for the else part, though I am not sure if that will mess up the file separator (forgot the default of PLINK)