Work around "Error: _____ cannot contain multiallelic variants." ?

[Konrad Taube]

Hi Christopher,

So I have gotten a smaller VCF file and am trying to convert it into .bed format. I have a new error and I'm wondering if there is a simple correction I can make to get the command to work? Here is what I can show you:

ktaube@phoebe:~/201105_AHLVWJDSXY/trimmed/vmac-only-final-minus3B1_outfiles$ plink2 --vcf oneout.recode.vcf --make-bed --allow-extra-chr --out vmac.recode

PLINK v2.00a2.3LM 64-bit Intel (24 Jan 2020)   www.cog-genomics.org/plink/2.0/

(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3

Logging to vmac.recode.log.

Options in effect:

  --allow-extra-chr

  --make-bed

  --out vmac.recode

  --vcf oneout.recode.vcf

Start time: Mon Jun 21 09:05:56 2021

515428 MiB RAM detected; reserving 257714 MiB for main workspace.

Allocated 193285 MiB successfully, after larger attempt(s) failed.

Using up to 192 threads (change this with --threads).

--vcf: 6857 variants scanned.

--vcf: vmac.recode-temporary.pgen + vmac.recode-temporary.pvar +

vmac.recode-temporary.psam written.

54 samples (0 females, 0 males, 54 ambiguous; 54 founders) loaded from

vmac.recode-temporary.psam.

6857 variants loaded from vmac.recode-temporary.pvar.

Note: No phenotype data present.

Writing vmac.recode.fam ... done.

Writing vmac.recode.bim ...

Error: vmac.recode.bim cannot contain multiallelic variants.

End time: Mon Jun 21 09:05:56 2021

Any suggestions would be really appreciated! Thanks so much,

[Christopher Chang]

Two options:

1. Filter those variants out with "--max-alleles 2".

2. Split them in advance with e.g. bcftools.

[Konrad Taube]

The former worked perfectly. Thanks so much!