VQSR or hard filters
Hi GATK team!
I was reading through the VQSR documentation. At some point it is stated that "Whole exome call sets work well, but anything smaller than that scale might run into difficulties." We used VQSR successfully for a 32Mb array and now I have an array of 20Mb.
I was wondering if this time the array is too small for the model. Shall I use hard filters instead?