Quickly learn what the identifiers are in any **BAM** dataset that is the result from mapping
Run Samtools: IdxStats on the aligned data (bam dataset).
The “index header” chromosome names and lengths will be listed in the output (along with read counts).
Compare the chromosome identifiers to the chromosome (aka “chrom”) field in all other inputs: VCF, GTF, GFF(3), BED, Interval, etc.
Note:
The original mapping target may have been a built-in genome index, custom genome (transcriptome, exome, other) – the same bam data will still be summarized.
This method will not work for “sequence-only” bam datasets, as these usually have no header.