Using -r2 in plink1.9 with .bim file that has CHR:POS entries

Question

[ethan.kreuzer]

Hello,

I have the following line of code:

/Plink1.9/plink --bfile "${PLINK_REF_PANEL}/${chrom}".final \
        --r2 \
        --ld-window 10000 \
        --ld-window-r2 ${PLINK_MIN_R2} \
        --keep "${PLINK_REF_PANEL_KEEP}" \
        --out "${out_prefix}" \
        --ld-snp-list "${SNAPTMP}/SNAP.input.proxy" \
         > plink.${chrom}.r2.out #/dev/null

And I have a .bim file that looks like this (head):

6     chr6:61725      0     61725       T      C
6     chr6:61754      0     61754       A      G
6     rs1333055309    0     61839       G      C
6     rs1345373303    0     61839       A      G

In my ".ld" file generated by the -r2 flag, I noticed there are only variants with rsid's and no variants with the "CHR:POS" labeling. Is this just anecdotal evidence or will the -r2 flag not calculate LD when the variant has no rsid. I want to be able to calculate LD even when a variant is identified as "CHR:POS". Thank you!

[Sam]

Does your ${SNAPTMP}/SNAP.input.proxy file contain SNPs with the CHR:POS identifier? PLINK will only calculate LD between SNPs in the --ld-snp-list. See documentation here

Answer 1

[chrchang523]

It's unrelated. PLINK makes no distinction between "rs" IDs and other types of variant IDs.