Variant Effect Predictor - Reverse/undo annotation

[MJ_McCabe]

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

[sarvidsson]

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.

[MJ_McCabe]

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