Plink error: Variant names are limited to 16000 characters.
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Entering edit mode
6 weeks ago
biyao.wang1 ▴ 10

Hi plink experts,

I'm trying to convert *.dose.vcf(.gz) files (product of the Michigan Imputation Server) to plink binary ones and got error since some snps has extremely long IDs. Does anyone know how to tackle this?

Commands I've tried in plink1.9 and 2:

--set-missing-var-ids @:#[b37] 
--set-all-var-ids  @:#[b37] 
--new-id-max-allele-len 
--vcf *.dose.vcf dosage=HDS 
--snps-only 
--biallelic-only 

I also tried DosageConvertor which has a function --trimNames but it resulted in dosage.gz, map, fam format files, which I don't know how to use...

I found very limited info online about this (see https://groups.google.com/g/plink2-users/c/u6nvaI1Olyg), it suggested to trim ID before converting in plink but did not exactly say how to do it.

Any suggestion will be appreciated! Many thanks in advance!

plink imputation • 123 views
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As it is a VCF file, maybe update the variant names before using plink, see below post:

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