Question: .stats file from vcf file with called variants - FilterMutectCalls (GATK)
gravatar for wiki97
8 weeks ago by
wiki970 wrote:

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:

statistic value

callable 2482690.0

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