What are the WES-specific settings when running GATK's variant recalibration step?

Question

[Joel Wallenius]

Hello,

while reading GATK's article here: https://gatk.broadinstitute.org/hc/en-us/articles/360035531112--How-to-Filter-variants-either-with-VQSR-or-by-hard-filtering

... they helpfully supply some default tranch values and suches for WGS data. They say that for WES and further detail we go to this article: https://gatk.broadinstitute.org/hc/en-us/articles/360035531612?id=1259

... and there is no mention of WES-specific settings. Amazing.

Am I missing something here? Are we supposed to guess some good values? I can't be the first to wonder this... but Google fails me. :(

Thanks in advance, Joel

[Mohamed]

Were you able to know the WES-specific settings?

Answer 1

[GenoMax]

https://gatk.broadinstitute.org/hc/en-us/articles/360036510892-VariantRecalibrator has an example of the command line for Exome data.