Convert Tab delimited file to VCF file

Question

[niharraul]

Hello,

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

[pld]

That looks pretty close to a VCF file, sans header and proper field names.

http://samtools.github.io/hts-specs/VCFv4.2.pdf

[stolarek.ir]

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

[Dataman]

It might be only enough to have ##fileformat=VCFv4.2 and the #CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tXXX.