Hi, I want to analyze exome-seq data. I already have vcf file with called variants, but those variants are not filtered and they are not annotated.
I would like to use GATK FilterMutectCalls and then annotate with Annovar. The problem is that GATK FilterMutectCalls needs a vcf.stats file, which is output from MuTect2 - and as I mentioned, I already have called variants in vcf file.
Do you know any tools which will allow me to create this stats file from a ready vcf file with called variants?
I would be grateful for any help :)
This is how this vcf.stats file looks like (it is from my other data analysis), it is a very short file: