Question: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
1
bsmith030465 • 170 wrote:
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 COMMENT
• link
•
modified 23 months ago
by
chrchang523 ♦ 7.7k
•
written
23 months ago by
bsmith030465 • 170