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.
gVCFs for Targeted Resequenced data
For targeted re-sequenced data, can we do variant calling using HaplotypeCaller in gVCF mode followed by using GenotypeGVCFs for joint genotyping ?
Would the following best practices work for targeted re-sequencing as well , except for VQSR as for targted resequencing GATK advices another way of filtering.