Question: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
1
gravatar for bsmith030465
8 months ago by
bsmith030465150
United States
bsmith030465150 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!

plink vcf • 879 views
ADD COMMENTlink modified 8 months ago by chrchang5235.8k • written 8 months ago by bsmith030465150
4
gravatar for chrchang523
8 months ago by
chrchang5235.8k
United States
chrchang5235.8k wrote:

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.)

ADD COMMENTlink written 8 months ago by chrchang5235.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2077 users visited in the last hour