Entering edit mode
5.1 years ago
jiangpeng59
▴
20
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:
After getting vcf and using hard filter, I found there is still too much varients, how can I remove more unrelated variants?
Mutect2 in gatk is the better choice in this situation?
Any help will be appreciated!