Hello,
I have a plink 2.0 file ("Ref" is always the major allele) and want to reorder its ref and alt alleles by a fasta reference. For this I use the --ref-from-fa command. However, the following error occurs:
Error: --ref-from-fa wants to change reference allele assignment at X:2700157,but it's marked `as 'known'. Add the 'force' modifier to force this change`
What does marked as "known" mean? How should I go on?
Best,
Andreas
•
written
by
Filago •
1 answer
plink 2.0 marks a reference allele as "provisional" instead of "known" when it comes from a plink 1 .bed file, or a VCF directly generated by plink from such a .bed file. Some of these reference alleles are expected to be wrong.
However, when a reference allele comes from a regular VCF file, it's expected to be correct; that's why an additional --ref-from-fa modifier is required to change it.
Yes, if you know the supposed REF alleles are really just major alleles, that's what "force" is for.
If I do so, I get the following report:
--ref-from-fa force: 4685 variants changed, 1 validated.
In total I only have 4686 variants...
The fasta reference which I use is from here: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz
And here is my command:
plink2 --pfile file --ref-from_fasta --fa reference.fasta --make-pgen --out output
What could be wrong here?
Thanks for your help!
Perhaps your original dataset had "backwards" alleles (with REF usually A1 instead of A2) for some reason, while still being correctly encoded. You can sanity-check this by running --freq on your updated dataset: if the alternate allele frequencies are usually low, you're probably fine.
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