query regarding Real Reference allele

[Palvi Malik]

Hello 

I am using the following command for retrieving data from SNPssek database. I want real ref alleles to be according to the real reference genome. Earlier, I was suggested to use --real-ref-alleles  option, but when I use that, there are approx 1100 SNPs in my genotypic file which have ref alleles not in accordance with reference genome. How can I solve this issue?

Command I used:

plink --chr-set 12 --allow-no-sex --bfile base_filtered_v0.7 --real-ref-alleles --keep Sativa_list.txt --geno 0.05 --mind 0.1 --maf 0.05 --recode vcf-iid bgz --out Selected-sativa

Thank you 

Palvi Malik

[Christopher Chang]

--real-ref-alleles is only for telling plink that you *already* have accurate reference alleles, and you want the exported VCF to omit the usual "reference allele may be wrong" annotations.

Since you only have SNPs, you should be able to set the reference alleles correctly with plink 2.0's --ref-from-fa command once you have the appropriate reference FASTA file.