```
samtools stats -h
```

Usage: samtools stats [OPTIONS] file.bam
       samtools stats [OPTIONS] file.bam chr:from-to
Options:
    -c, --coverage <int>,<int>,<int>    Coverage distribution min,max,step [1,1000,1]
    -d, --remove-dups                   Exclude from statistics reads marked as duplicates
    -X, --customized-index-file         Use a customized index file
    -f, --required-flag  <str|int>      Required flag, 0 for unset. See also `samtools flags` [0]
    -F, --filtering-flag <str|int>      Filtering flag, 0 for unset. See also `samtools flags` [0]
        --GC-depth <float>              the size of GC-depth bins (decreasing bin size increases memory requirement) [2e4]
    -h, --help                          This help message
    -i, --insert-size <int>             Maximum insert size [8000]
    -I, --id <string>                   Include only listed read group or sample name
    -l, --read-length <int>             Include in the statistics only reads with the given read length [-1]
    -m, --most-inserts <float>          Report only the main part of inserts [0.99]
    -P, --split-prefix <str>            Path or string prefix for filepaths output by -S (default is input filename)
    -q, --trim-quality <int>            The BWA trimming parameter [0]
    -r, --ref-seq <file>                Reference sequence (required for GC-depth and mismatches-per-cycle calculation).
    -s, --sam                           Ignored (input format is auto-detected).
    -S, --split <tag>                   Also write statistics to separate files split by tagged field.
    -t, --target-regions <file>         Do stats in these regions only. Tab-delimited file chr,from,to, 1-based, inclusive.
    -x, --sparse                        Suppress outputting IS rows where there are no insertions.
    -p, --remove-overlaps               Remove overlaps of paired-end reads from coverage and base count computations.
    -g, --cov-threshold <int>           Only bases with coverage above this value will be included in the target percentage computation [0]
      --input-fmt-option OPT[=VAL]
               Specify a single input file format option in the form
               of OPTION or OPTION=VALUE
      --reference FILE
               Reference sequence FASTA FILE [null]
  -@, --threads INT
               Number of additional threads to use [0]
      --verbosity INT
               Set level of verbosity
