I tried to convert a VCF file to bed/bim/fam format with PLINK v1.90b3.31 64-bit (3 Feb 2016) plink2
And the parameters are listed below:
--vcf test.vcf \
--vcf-idspace-to _ \
--allow-extra-chr 0 \
--split-x b38 no-fail \
Unfortunately, however, plink2 stopped and reported error like this:
Error: Variant names are limited to 16000 characters.
I guess some variants in my VCF file have a very long name. Because the variant name is comprised of it's POS and REF/ALT alleles, which maybe too long.
Anyone knows how to solve this problem? I want a simple solution, just like using some special parameters of plink