vcftools: the of number of position does not match the number of columns of genotypes

[Mike_Brown]

Hello!
I have vcf.gz file, and I want to change it into 012 matrix. I use follow command

vcftools --gzvcf chr1.vcf.gz --out chr1 --012

Then, it outputs chr1.012, chr1.012.pos, and chr1.012.indv. But I found the length of each row of chr1.012 is not equal. And the length of rows of chr12.012 is not same as chr1.012.