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Panel of Normals for RNA-Seq Samples

Brunods10Brunods10 AugustaMember
Hello. Is it appropriate to use the 1000g panel of normals (1000g_pon.hg38.vcf.gz) when working with RNA-Seq samples? I've been looking for more information about the 1000g PoN and have not found much.

Specifically, I am using the 1000g PoN in tumor-only mode with RNA-Seq tumor samples. I have used STAR 2-pass alignment and the somatic variant calling best-practices pipeline on a few dozen samples. I unexpectedly saw hundreds of variants shared by the samples. Is there anything wrong with using the 1000g PoN with RNA-Seq generated BAM files in tumor-only mode?

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