convention from vcf to plink

Question

[boymin2020]

Hi, I want to just keep SNPs during the vcf2plink conversion, this is the command:

plink1.9 --noweb --vcf ${vcf_fil} --double-id --biallelic-only --snps-only just-acgt --make-bed --out

The error is

Error: Invalid --snps-only parameter ‘just-acgt’.

Does anyone encounter the same issue. If yes, could you tell me the solution?

[Ram]

just-acgtis new to 1.9. If you're sure you're using the right version, try 'just-acgt' instead of just-acgt (pay attention to the quotes)

[boymin2020]

I tried, nothing changed.

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

[boymin2020]

Got it, thanks for the tips.

Answer 1

[chrchang523]

Switch to a more recent plink 1.9 build; this modifier was renamed from “no-DI” to “just-acgt” several years ago.