Flipped $ref and $alt when converting plink binary files to gds format

[ryshi06]

No description provided.

[ryshi06]

Hi, I was trying to convert plink binary files to gds with the command

SeqArray::seqBED2GDS(bed.fn, fam.fn, bim.fn, out.gdsfn, compress.geno="LZMA_RA", compress.annotation="LZMA_RA", chr.conv=TRUE, optimize=TRUE, digest=TRUE, parallel=FALSE, verbose=TRUE),

the command works for most of the SNVs, but it failed for some SNVs as it flipped the ref and alt. For example, the SNV rs12404190 has bim record: 1 rs12404190 0 105020628 G A, and from dbSNP, it shows the reference allele should be G, and the alt should be A. However, when I used the following command to rename the SNPs, it gives me 1-105020628-A-G.

CHR <- as.numeric(seqGetData(genofile, "chromosome")) position <- as.integer(seqGetData(genofile, "position")) REF <- as.character(seqGetData(genofile, "$ref")) ALT <- as.character(seqGetData(genofile, "$alt")) VarInfo_genome <- paste0(CHR,"-",position,"-",REF,"-",ALT)

Is there a way to fix this? Thanks!

Best,
Ruyu

[zhengxwen]

Currently, SeqArray has no function to flip the reference and alternative alleles.
You could flip the alleles using PLINK, e.g, https://www.cog-genomics.org/plink/2.0/data#ref_allele

In the early version of PLINK, the allele columns in BIM are defined as the minor and major.
The recent version of PLINK has allowed users to use the ref and alt in the BIM file.