Tag: file-formats

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 genome reader is really three things: the sequencer that produces reads, the aligner and variant caller that turn reads into a genome, and the browser that lets you look at it. Here is what each step produces, which tools we would run, and where they fail.