Entering edit mode
7.6 years ago
niharraul • 0
I have tab delimited/csv file containing the SNP information and want to convert it to vcf file so that I can annotate it using VEP
chromosome Number chromosome position SNP ids Ref Allele Alt Allele Qual Filter Info 21 26960070 rs116645811 G A . . . 21 26965148 rs1135638 G A . . . ... ...
I am familiar with python. It will be great if you could provide any suggestion/help
That looks pretty close to a VCF file, sans header and proper field names.
Just copy header from some VCF file. Just make sure to have information fields ('#') that matches your fields, and chromosome lengths.
Or read on vcf-annotate, which I was using to make vcfs with custom fields some time ago
It might be only enough to have