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Discrepancy between sequence alignment and variant calling reference (hg38), WGS processing

I'm processing a whole genome sequencing dataset, where the sequence alignment step was performed in BWA using UCSC's version of the hg38 reference genome (hg38.fa: https://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/). However I'm currently running GATK4's HaplotypeCaller on these samples using the recommended reference from the GAKT bundle (Homo_sapiens_assembly38.fasta: https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0;tab=objects?pli=1&prefix=&forceOnObjectsSortingFiltering=false), and I had originally planned to continue using this reference for the subsequent GenotypeGVCFs and VQSR filtering steps. Is this discrepancy trivial, or do I need to run all variant calling/joint-genotyping/filtering steps using the UCSC reference version for consistency? I'm running GATK version 4.2.0.0 on a LSF cluster system.

alignment sequencing calling gatk4 sequence reference whole variant genome hg38
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written by karen.therrien • karen.therrien

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