I have short read exome data. For creating intervals, I converted the reference fasta file to reference bed file and used this bed file as list of intervals. I used this intervals list for storing all the GVCF files in the database (https://gatk.broadinstitute.org/hc/en-us/articles/360036883491-GenomicsDBImport). Will using the interval list from reference genome lead to error in subsequent steps?. Please advice
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