The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
SNP and INDEL VariantFiltration Parameters
I've been looking for recommended filter expressions for SNP and INDEL variant filtration. I found these articles on the topic: one and two. I noticed that in the second article the SOR annotation is recommended for both SNP and INDEL filtration, while in the first article it is not. I would like to know which of these filter expressions would be considered Best Practice for variant filtration.