Which reference should I use for my analyses?
The reference "GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz" (GRCh38_verily) from https://cloud.google.com/life-sciences/docs/resources/public-datasets/reference-genomes seems to be reasonable but all pipelines from Terra/GATK refers to the "original" GRCh38.
Will it be a big "faux pa" if I use "GRCh38_verily" instead of the "original" one? Will I have problems in downstream analyses?
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