Finding BAM dataset identifiers
Quickly learn what the identifiers are in any **BAM** dataset that is the result from mapping
- Run Samtools: IdxStats on the aligned data (
- 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.
- The original mapping target may have been a built-in genome index, custom genome (transcriptome, exome, other) – the same
bamdata will still be summarized.
- This method will not work for “sequence-only”
bamdatasets, as these usually have no header.