Convert Tab delimited file to VCF file
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
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niharraul •
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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
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
##fileformat=VCFv4.2and the#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tXXX.