PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
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!
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chrchang523
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bsmith030465
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bsmith030465
1 answer
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.)
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