convert a SAM file to a BAM file
samtools view -b -S SAMPLE.sam > SAMPLE.bam
  -S Input is in SAM format
  -b Output in BAM format

convert a BAM file to a SAM file
samtools view -h SAMPLE.bam > SAMPLE.sam

sort a BAM file

samtools sort SAMPLE.bam -o SAMPLE_sorted.bam

# using a unix pipe (input '-')

cat SAMPLE.bam | samtools sort - -o SAMPLE_sorted.bam

samtools sort SAMPLE.bam SAMPLE   # old version v1.2

sort by readName
samtools sort -n SAMPLE.bam -o SAMPLE_sorted.bam

Stats

get number of reads

(number of individual reads, paired reads that mapped both count double R1+R2)
samtools view -c SAMPLE.bam

more statistics about alignments
samtools flagstat SAMPLE.bam

comprehensive statistics
samtools stats SAMPLE.bam

Get coverage

# get coverage of a selected region (e.g., from base 1,958,700 to 1,958,907 of a contig)
samtools index sampleID.bam
samtools mpileup -r 'contigName:1,958,700-1,958,907' sampleID.bam
# same in combination with awk to count the total and averaged coverage
samtools mpileup -r 'contigName:1,958,700-1,958,907' sampleID.bam | awk 'BEGIN{C=0}; {C=C+$4}; END{print C "\t" C/NR}'

see also: → Calling SNPs/INDELs with SAMtools/BCFtools

Note: SAMtools mpileup counts only primary aligned reads. SAMtools discards unmapped reads, secondary alignments and duplicates. To consider also secondary alignments, BEDtools could be an alternative.

Introduction by Dave Tang