Question: What is ploidy level for HaplotypeCaller ?
gravatar for mirzaei86.vahid
2.6 years ago by
mirzaei86.vahid30 wrote:

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

snp gatk genome • 1.1k views
ADD COMMENTlink modified 2.6 years ago by WouterDeCoster42k • written 2.6 years ago by mirzaei86.vahid30
gravatar for WouterDeCoster
2.6 years ago by
WouterDeCoster42k wrote:

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

ADD COMMENTlink written 2.6 years ago by WouterDeCoster42k
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