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Extracting variations in the gene regions and from 100 bp of gene boundary from multiple VCF files

Hi,

I sincerely hope that I am not repeating an already answered question. I couldn't find the answer to my exact problem.

I have three VCF files derived using bcftools (isec). Those three files contain similar variations compared to the reference sequence. End of the day, I have

  • Three VCF files representing three varieties (include only the common variations)
  • Reference FASTA file
  • Annotation (gff3) file for reference.

What I want to do is extract variations found in;

  1. Gene region
  2. 100 bp from TSS/+1 and the stop codon

Please note this is a 5 MB region (not a whole-genome, so there are no chromosomes).

I appreciate it if someone can help me in this regard. Thank you!

vcf variations
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updated by Tm Tm • written by VenGeno • VenGeno

1 answer

You can try using variant annotation tools like snpeff. It will add gene-related information (exonic, intronic, intergenic etc) in your vcf file.

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written by Tm Tm

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