Convert Tab delimited file to VCF file
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Entering edit mode
6.1 years ago
niharraul • 0

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

 

 

 

 

snp • 6.0k views
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3
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That looks pretty close to a VCF file, sans header and proper field names.

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

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1
Entering edit mode

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

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

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