What is ploidy level for HaplotypeCaller ?
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
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mirzaei86.vahid •
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Humans are diploid, so ploidy = 2, which is the default setting so you don't have to specify this.
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