Deleted:Dealing with multiallelic variants in PLINK merge

Question

[Lloyd_641]

I was trying to merge UK biobank imputed array data of different chromosomes (PLINK binary filesets) to apply quality control, and was not sure what to do with multiallelic variants.

I have tried using PLINK1.9 with the flag --biallelic-only but it proved only useful for vcf files. The flag --max-alleles 2 was unrecognized by PLINK1.9 as well. The error says

Error: 328622 variants with 3+ alleles present.
* If you believe this is due to strand inconsistency, try --flip with ./missnp
(Warning: if this seems to work, strand errors involving SNPs with A/T or C/G alleles probably remain in your data. If LD between nearby SNPs is high, --flip-scan should detect them.)
*If you are dealing with genuine multiallelic variants, we recommend exporting that subset of the data to VCF (via e.g. '--recode vcf'), merging with another tool/script, and then importing the rusult; PLINK is not yet suited to handling them.

As suggested, I have tried

plink \ #1.9b
    --merge-list mergeBED.lsit \
    --recode vcf \
    --out chrall

but it returned the same error.

Does anyone know what I should do about this? Deeply appreciated!