Can plink r2 results output ref/alt allele info?

[Lynn Yang]

Hello, 

I hope you're doing well. I am new to Plink, and would like to get a list of SNPs in LD with a tag SNP, along with the SNPs' reference and alternative allele information.

 I used this code to get the list of SNPs in LD with rs2164624:

./plink --bfile EUR_hg38_chr10 --r2 --ld-snp  rs2164624 --with-freqs

Could you let me know if there is any flag to add allele information? 

Some additional info: I followed instructions to download the reference from: https://www.cog-genomics.org/plink/2.0/resources#1kg_phase3, and converted it to .bed, .bim, and .fam files. My bfile is one that I filtered for EUR.

Thank you so much for your help! I appreciate it very much. 

Best,

Lynn

[Christopher Chang]

1. The simplest way to add allele info for now is to change the variant IDs to include them.  If you're willing to replace the rsIDs with position+allele-based IDs, plink 2.0's --set-all-var-ids flag will do the trick; alternatively, you could write a short script to modify the .bim file in the necessary manner.

2. --r2-phased and --r2-unphased should be implemented in plink 2.0 within the next month, and they will support optional REF/ALT column-sets.