I have an issue working with vcf files in that when I rename entries with no ID to be CHR:POS:REF:ALT, the ID's produced are sometimes too long when converted to plink .bed files. I do not want to change the name convention to something different than CHR:POS:REF:ALT and I do not want to removed them. Is there away to filter out entries in VCF files such that if their ID's are longer than say, 15 characters, they get removed ?
Example, the following entries with these ID's will be kept:
rs145699 rs343930204 chr6:10550:A:T chr6:54032:G:C
The following would be removed:
I am looking for a command that uses bcftools to do this ideally. Thank you!