I am using Mutect2 184.108.40.206 for somatic variant calling using af-only-gnomad.vcf.gz (gatk resource bundle) as germline resource.
I found the default setting of --af-of-alleles-not-in-resource -1.0 for variant calling.
This is mentioned on the Mutect2 page:
"Starting with v220.127.116.11, GATK recommends the default setting of --af-of-alleles-not-in-resource, which the tool dynamically adjusts for different modes. tumor-only calling sets the default to 5e-8, tumor-normal calling sets it to 1e-6 and mitochondrial mode sets it to 4e-3. For previous versions, the default was 0.001, the average heterozygosity of humans".
I am assuming above defaults value are valid in case of variant calling without germline resources.
But when I am running say, tumor-only mode --af-of-alleles-not-in-resource value remains -1.0 in the command line of vcf file. So, how will I know the tool dynamically adjusts the defaults for different modes? Or, I need to change the defaults value to 5e-8 for tumor-only mode.
Secondly, in the case of af-only-gnomad.vcf.gz (gatk resource bundle) as germline resource for variant calling. Shall I change --af-of-alleles-not-in-resource value to recommended value 0.0000025 irrespective of variant calling modes, tumor-only or tumor-normal ?
Please clarify my doubts.
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