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

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...

Any suggestion will be appreciated! Many thanks in advance!

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Entering edit mode

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