What is ploidy level for HaplotypeCaller ?

Question

[mirzaei86.vahid]

Dear all,

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?

Regards, Vahid

Answer 1

[WouterDeCoster]

Humans are diploid, so ploidy = 2, which is the default setting so you don't have to specify this.