I got vcf file from my instructor. It is VEP annoted with over 50 options separated by ||. I noticed that the vcf is not arrange to appropriate columns so I decided to sort it.
I used this code to sort my vcf file according position:
$ grep "^#" input.vcf > output.vcf $ grep -v "^#" input.vcf| sort -k1,1V -k2,2g >> output.vcf
However after I used it I expected to have output.vcf data sorted into columns. Instead all data of each variant data is still shift.
Am I doing something wrong? Is it different way to arrange vcf into columns?