Samtools

# 2) Sort and index a BAM
samtools sort -@ 8 -o sample.sorted.bam sample.bam
samtools index sample.sorted.bam

# 3) Inspect basic mapping statistics
samtools flagstat sample.sorted.bam
samtools stats sample.sorted.bam > sample.stats.txt

# 4) Extract one region
samtools view sample.sorted.bam chr1:100000-110000

Recommended Workflow

1. Convert aligner output into BAM or CRAM as needed.
2. Sort the file before indexing or region-based access.
3. Run flagstat, stats, coverage, or depth to sanity-check the alignment.
4. Use specialized subcommands like fastq, fasta, faidx, or dict only when the workflow specifically needs them.

Guardrails

• Region-based operations require sorted and indexed files.
• samtools quickcheck is a cheap integrity test before burning compute on a broken BAM/CRAM.
• Use -@ for thread-aware subcommands, but do not assume every subcommand parallelizes the same way.
• Be explicit about output format and destination; many subcommands default to stdout.