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How to sort vcf file

Here is a screenshot of my VCF and I want to extract info from an extra column put in each value in a separate column like a standard VCF file!

Thanks in advance!

vcf
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written by shubhamkumbhar420 • shubhamkumbhar420

1 answer

the correct answer would be

bcftools sort your.vcf

but your image shows that it is not a VCF file. The last VCF header should be #CHROM POS ID REF ALT QUAL FILTER INFO... so It's something else... with a VCF header (##).

and the usual associated image:

enter image description here

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written by Pierre Lindenbaum Pierre Lindenbaum

yeah! The VCF file is annotated with 1)snpEff and 2)VEP (variant effect predictor). Now I want to separate the fields. !!!

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written by shubhamkumbhar420 • shubhamkumbhar420

Now I want to separate the fields. !!!

? that's not sorting a vcf

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written by Pierre Lindenbaum Pierre Lindenbaum

I mean extract the fields. and it's not a proper VCF cause this is generated by VEP (ensemble).

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written by shubhamkumbhar420 • shubhamkumbhar420

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