Samtools

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 # From http://www.htslib.org/doc/samtools.html
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 samtools view -bt ref_list.txt -o aln.bam aln.sam.gz
 samtools sort -T /tmp/aln.sorted -o aln.sorted.bam aln.bam
 samtools index aln.sorted.bam
 samtools idxstats aln.sorted.bam
 samtools flagstat aln.sorted.bam
 samtools stats aln.sorted.bam
 samtools bedcov aln.sorted.bam
 samtools depth aln.sorted.bam
 samtools view aln.sorted.bam chr2:20,100,000-20,200,000
 samtools merge out.bam in1.bam in2.bam in3.bam
 samtools faidx ref.fasta
 samtools tview aln.sorted.bam ref.fasta
 samtools split merged.bam
 samtools quickcheck in1.bam in2.cram
 samtools dict -a GRCh38 -s "Homo sapiens" ref.fasta
 samtools fixmate in.namesorted.sam out.bam
 samtools mpileup -C50 -gf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam
 samtools flags PAIRED,UNMAP,MUNMAP
 samtools fastq input.bam > output.fastq
 samtools fasta input.bam > output.fasta
 samtools addreplacerg -r 'ID:fish' -r 'LB:1334' -r 'SM:alpha' -o output.bam input.bam
 samtools collate aln.sorted.bam aln.name_collated.bam
 samtools depad input.bam
 samtools markdup in.algnsorted.bam out.bam