I have a BAM file containing an alignment to the GRCh38 "analysis pipeline" set with decoys (from ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/ seqs_for_alignment_pipelines/).
I remapped NCBI's "resource bundle" VCF files to UCSC's hg38 using a combination of UCSC's chain files, CrossMap, and custom scripts. I want to run GATK indel realignment, base calibration, and variant calling on my BAM file using some of these remapped VCF files (e.g. -known on RealignerTargetCreator).
The BAM and VCF come from different assemblies (GRCh38 with decoys and hg38, respectively). I can change GRCh38 chromosome names to hg38 chromosome names (NCBI provides a map), but is this sufficient to ensure that tools interpret the VCF files' coordinates correctly?