How does plink guess the reference base in "--recode vcf-iid"

Question

[Dan]

Here: http://oryzasnp-atcg-irri-org.s3-website-ap-southeast-1.amazonaws.com/3krg-3k_filt_snp-v1/README-3kRG-filtered-SNP-v1.txt

The recommended SOP for recoding PED / MAP to VCF is:

plink --file <ped file name without extension> --recode vcf-iid --out <output file name without extension>

However, without specifying the reference sequence, how is the reference base in the VCF guessed?

Does plink have an extra option for passing the reference sequence when calling --recode?

I'm reading about the associated file formats here:

• http://pngu.mgh.harvard.edu/~purcell/plink2/formats.html#map
• http://pngu.mgh.harvard.edu/~purcell/plink2/formats.html#fam
• http://pngu.mgh.harvard.edu/~purcell/plink2/formats.html#ped

and I don't see the reference base stored anywhere.

Answer 1

[Dan]

From plink --help | less

  --recode ...

    The A2 allele is saved as the reference and normally flagged as not based
    on a real reference genome ('PR' INFO field value).  When it is important
    for reference alleles to be correct, you'll also want to include
    --a2-allele and --real-ref-alleles in your command.

  --a2-allele [filename] {a2col} {IDcol} {skip} :
    Force alleles in the file to A2.  ("--a2-allele [VCF filename] 4 3 '#'",
    which scrapes reference allele assignments from a VCF file, is especially
    useful.

Sigh