https://community.dnanexus.com/s/question/0D582000001cFXNCA2/how-can-i-convert-vcf-file-to-tabular-data I got an exported table file using the code in the response to the question that link that I share. But there are not informations of the format section of VCF file in the exported table's columns. When I preview the VCF file in the folder in UKB RAP, I can see informations of format section. I share the screenshot of the preview of the VCF file. I want to change on the code in order to the exported table to contains informations of format section too, but I couldn't. Could you help me a little on this?
[Image: Ekran Resmi 2023-08-22 10.44.16]
Hello @Burcu Çevik?, if I understand this correctly, this is question more about how to format/rename columns in your dataframe/table to have better representation (or "human readable" if you will), not much about working with variants itself. This sounds like a doable data operation, indeed. I would first export rows that begins with ##INFO string (you can do it in bash using grep) and then it would need a bit of programming work to map that metadata to your existing pandas dataframe (based on order of columns or column names, not sure how you store it) and rename.
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You can also use bcftools --annotate to extract information from INFO column of a VCF file.
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Many thanks for your suggestion. Is there any command line that you recommend to I use with Swiss Army Knife?
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Hello @Burcu Çevik?, if I understand this correctly, this is question more about how to format/rename columns in your dataframe/table to have better representation (or "human readable" if you will), not much about working with variants itself. This sounds like a doable data operation, indeed. I would first export rows that begins with ##INFO string (you can do it in bash using grep) and then it would need a bit of programming work to map that metadata to your existing pandas dataframe (based on order of columns or column names, not sure how you store it) and rename.
You can also use bcftools --annotate to extract information from INFO column of a VCF file.
Many thanks for your suggestion. Is there any command line that you recommend to I use with Swiss Army Knife?
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