Tag: bam

A field-by-field guide to the eleven mandatory SAM/BAM columns, the optional tags that matter, and the commands to read, filter, and visualize your own alignments.

An annotated alignment record from a 30x human whole-genome BAM, plus the samtools commands we use to inspect a new file and the failure modes worth checking first.

A practical guide to opening and inspecting BAM alignment files: samtools on the command line, IGV for visual review, and the checks worth running before you trust a variant call.

A practical setup for loading your own WGS alignments, variant calls, and RNA-seq coverage into IGV and igv.js, with the indexing, reference-build, and chromosome-naming details that usually break first.