I have failed convert vcf to Plink(v1.07) format

[Wusun5]

Respectly MareesAT :

When I running the command, plink --vcf ALL.2of4intersection.20100804.genotypes.vcf.gz --make-bed --out ALL.2of4intersection.20100804.genotypes, I have got the work-log below:

@----------------------------------------------------------@ | PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------|

(C) 2009 Shaun Purcell, GNU General Public License, v2
For documentation, citation & bug-report instructions:
http://pngu.mgh.harvard.edu/purcell/plink/
@----------------------------------------------------------@

Web-based version check ( --noweb to skip ) Recent cached web-check found...Problem connecting to web

Writing this text to log file [ ALL.2of4intersection.20100804.genotypes.log ] Analysis started: Wed Sep 14 16:15:57 2022

** Unused command line option: --vcf ** Unused command line option: ALL.2of4intersection.20100804.genotypes.vcf.gz

ERROR: Problem parsing the command line arguments.

Could you please solve it ?

All's best!

[Truongphi20]

Try to use plink2 instead

plink2     --vcf ALL.2of4intersection.20100804.genotypes.vcf.gz \
             --make-bed \
             --max-alleles 2 \
             --out ALL.2of4intersection.20100804.genotypes

[!NOTE] --max-alleles 2 to avoid multi-allelic error (cause the original VCF file contains)