GATK VQSR for human WGS

Question

[quentin54520]

Hello all,

I'm working with human WGS data from germline for rare disease.

I'm a bit lost for the VQSR step because the command (option) are not the same between the tool page and the tuto page.

I don't really understand the differences i use the option --tranches or not.

Maybe someone could give me a good "classic" method for these type of human data? Or maybe just used the default parameters ?

Thanks in advance

[samuelandjw]

I recommend following the tutorial page, which teaches you to run VQSR meaningfully.