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I'm trying to prepare my customized pon file for my 19 WES data. I followed https://gatk.broadinstitute.org/hc/en-us/articles/360046224491-CreateSomaticPanelOfNormals-BETA- However, with all the exon regions (for the NimbleGen ExomeV3+UTR kit), the gatk GenomicsDBImport was really slow and failed to complete because run out of all the disk space. Can I just split the region bed file into multiple bed files and then fuse all the vcf files together for Mutect2 variant calling? Also should I merge the pon file derived from my own data with the public GATK panels of normals (1000g_pon.hg38.vcf.gz)?
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