Hello, I am a fresh in gatk, I got some samples from different patient at different phase. for exmaple:
normal phase : 1 patient sample
tumor phase1 : 9 patient samples
tumor phase2 : 7 patient samples
tumor phase3 : 10 patient samples

I went to attain the variants at different phases, by reading the gatk best practice, I have finished joint calling to each phase (CombineGVCFs+GenotypeGVCFs) .
I get two questions following:

1. After getting vcf and using hard filter, I found there is still too much varients, how can I remove more unrelated variants?

2. Mutect2 in gatk is the better choice in this situation?

Any help will be appreciated!