Attention: Want an end-to-end pipelining solution for GATK Best Practices?
You can follow my NGS tools from docker hub keyword skysbiodocker.
- Last Active
- Full Name
- Gökalp Çelik
You need java version 1.8 for GATK to run. You are using version 11 which is not compatible with GATK. (View Post)
Before going into any threshold filters I would go simply for transmission and genotyping data from trios. whether a particular variant is called or not. if called is it homozygous or heterozygous re… (View Post)
Pretty much normal. However joint genotyping this way is not the suggested approach. It is better and more feasible (both computationally and time wise) to genotype in GVCF mode and do joint genotypi… (View Post)