Ann.vcf format

Question

[JAZMIN CELESTE]

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

[Pierre Lindenbaum]

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

Want to know something terrifying? There are people currently analysing whole exome variant data using Excel. I kid you not.

— Daniel MacArthur (@dgmacarthur) October 25, 2012

Answer 1

[raphael.B]

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 :)

[JAZMIN CELESTE]

Thank you so much :D