Are there any repository for panel of normal for running Mutect2?
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9 months ago
dare_devil ★ 1.5k

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
Mutect2 PON panel of normal gatk • 327 views
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Publicly Available WGS Samples for Panel of Normals? and many other threads, please use the search function before posting.

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