I plan on using Mutect2 to call somatic variants for WGS. The alignment and sorting is already performed by the core facility, which uses the GRCh37.p13 reference genome. For optimal performance a panel of normals should be used when running Mutect2, however as far as I know there is no publicly available panel of normals for the GRCh37. However, there is a panel of normals for b37 (https://console.cloud.google.com/storage/browser/_details/gatk-best-practices/somatic-b37/Mutect2-WGS-panel-b37.vcf). I was wondering if you think, that I can take this panel of normal, regardless of the slight differences ( https://gatk.broadinstitute.org/hc/en-us/articles/360035890711-GRCh37-hg19-b37-humanG1Kv37-Human-Reference-Discrepancies) in the reference genome.
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