I have rudimentary questions about GATK pipline:
First about HaplotypeCaller , I have set -ploidy 1 , my sample belong to human specie.
Is it correct to set ploidy=1 for human?
I'm working on germline mutation but I saw different pipeline for somatic mutation in GATK best practice,I'd like to know for finding somatic mutation we should have at least >=2 samples to make comparison right?
And What is the best tool in GATK for somatic mutation?