Are there any repository for panel of normal for running Mutect2?
I am trying to call somatic mutations from tumor sample where I don't have any normal sample. Are there any repository for panel of normal or a downloadable file like pon.vcf.gz
gatk4_mutect2_4136_pon.vcf.gz
I want to run
gatk Mutect2 -R hg38.fa \
-I input_tumor.bam \
-pon gatk4_mutect2_4136_pon.vcf.gz \
--germline-resource af-only-gnomad.hg38.vcf.gz \
--af-of-alleles-not-in-resource 0.0000025 \
--genotype-germline-sites \
-L exome_autoXYM.intervals \
-O mt2_unmatched.vcf.gz
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