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  • Variant Effect Predictor - Reverse/undo annotation

    Hello all.
    I'm quite new to bioinformatics but having a lot of fun with it.
    I sometime back annotated a vcf using VEP. For compatibility reasons, I need to redo this, but have lost the vcf!

    So, I wonder if anybody knows how to reverse or undo the annotation of a .vep.vcf file to give me back the original vcf? I assume this would involve using awk or sed, but would appreciate some detailed help considering my lack of experience!

    Many thanks for your time and effort.

    Kind regards

    Mark

  • #2
    Not familiar with the exact format VEP outputs, could you post a couple of data lines from it? I'd assume that it simply adds a INFO field tag, which could be removed by sed.
    Last edited by sarvidsson; 02-26-2015, 12:32 AM. Reason: grammar

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    • #3
      Thank you very much for your reply. I think you are correct that it involves sed. The only two lines which differentiates it from a vcf is the info line as well as the vep line above it. I did sed it and have used vep to re-annotate using the current version. Hopefully this will now work! But here are some of the lines to see if you would agree with what I did

      Thanks again!

      ##contig=<ID=GL000193.1,length=189789,assembly=b37>
      ##contig=<ID=GL000194.1,length=191469,assembly=b37>
      ##contig=<ID=GL000225.1,length=211173,assembly=b37>
      ##contig=<ID=GL000192.1,length=547496,assembly=b37>
      ##reference=file:///home/marmcc/Clinical_Genomics_Pipeline/runs/Panel/Panel_run_Dec_2014/paddy/pipeline/tools/biodata_gi/gatk-resource-bundle/2.8/b37/human_g1k_v37.fasta
      ##source=SelectVariants
      ##VEP=v76 cache=/share/ClusterShare/biodata/contrib/gi/vep/homo_sapiens/76_GRCh37 db=.
      ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Consequence|Codons|Amino_acids|Gene|HGNC|Feature|EXON|PolyPhen|SIFT">
      #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT

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