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Ann.vcf format

Hello everyone!

I used a pipeline named Sarek to run my WES data. The pipeline used two programs to annotate VEP and SnpEff and give to me an ann.vcf file.

I don't know how to use or open this file in excel for do the filters and choose the variants of interest. I tried to open it in excel but the headers doesn't match with columns so I don't know which column is each one. Do you know about a program to convert VCF into CSV? or maybe how can I access to this files, to see the annotation and do the manual filters? Thank you

vcf vep snpeff annotation
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written by JAZMIN CELESTE • JAZMIN CELESTE

I don't know how to use or open this file in excel for do the filters and choose the variants of interest.

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written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

Hello, VCF is a file format dedicated to variant analysis. It is not a good practice to process it with excel. You can have a look at bcftools, which allows to perform a wide range of operation on VCF. For example, checking if 'missense' is in the ANN field : bcftools view -i 'ANN~"missense"' input.vcf.

Good luck :)

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written by raphael.B • raphael.B

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