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Options GATK4 HaplotypeCaller vs Varscan

oxidizeroxidizer ZürichMember

I'm new with GATK. I usually use Varscan for variant calling with the following options :

--min-coverage 7 --min-reads2 7 --min-var-freq 0.80 --variants

Which options I have to use with Gatk 4 HaplotypeCaller for similar results?

Answers

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