Convert Tab delimited file to VCF file
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9.0 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             .       .         .
...
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I am familiar with python. It will be great if you could provide any suggestion/help

snp • 10.0k 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
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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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