Visual summary from a collection of .vcf files (WES)

Question

[Angel]

Hi guys,

I was wondering whether there is any available software to produce a visual summary from a collection of annotated .vcf files (say, the output of VEP). Something similar to the left panel in this figure, which includes total number of variants, number of samples in which the gene has been found mutated, functional impact, etc.

Thank you!

Edit: corrected typo, VEF --> VEP

[brunobsouzaa]

How you annotate your VCFs? Ensembl VEP will output this for you, just use the --stats_file on the command line during annotation.

[Angel]

I use VEP (there was a typo in my original message), I was just wondering if there is a tool to generate visual summaries in an easy way.

Answer 1

[Ram]

Check out maftools. It is built for cancer datasets but can be used with any annotated VCF. You will need to use bcftools query to get the necessary columns from the VCF file.

[Angel]

That´s exactly my use case, thank you!