Hi,

I am trying to convert a vcf.gz file to bed/bim/fam format using PLINK2 (data is hg38).

My command is: 

    plink2 --vcf variants.vcf.gz --out variants --freq --make-bed --chr 1-22 XY

I get an error:

    Error: Invalid chromosome code 'chr11_KI270721v1_random' on line 36088290 of

How can I ensure that I filter out these variants/sequences?

thanks!
Add the "--allow-extra-chr" (or "--aec" for short) flag to permit these codes in the input.  (--chr 1-22 XY will then filter them out.)