What the columns in a BAM file mean
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.
Tag: samtools
6 posts
A Real BAM File Example, Field by Field
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.
How to View a BAM File
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.
Aligning Your Whole-Genome FASTQs with BWA-MEM
A step-by-step guide to indexing a human reference, running bwa mem on 30x whole-genome FASTQs, and producing a sorted CRAM for variant calling.
How to Read Your Own DNA Sequence From Raw Files
A practical walkthrough of going from FASTQ, BAM/CRAM, and VCF files to an actual nucleotide sequence you can read, translate, and check against the reads it came from.
How to Use WGS Extract, and When to Use samtools Instead
A working guide to verifying, converting and analyzing a personal 30x whole-genome file. Covers the reference build, CRAM to BAM and coverage QC.