```bash
docker run --rm quay.io/biocontainers/bcftools:1.22--h3a4d415_1 bcftools stats --help 2>&1 | grep -v unrecognized
```

About:   Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats.
         When two files are given, the program generates separate stats for intersection
         and the complements. By default only sites are compared, -s/-S must given to include
         also sample columns.
Usage:   bcftools stats [options] <A.vcf.gz> [<B.vcf.gz>]

Options:
        --af-bins LIST               Allele frequency bins, a list (0.1,0.5,1) or a file (0.1\n0.5\n1)
        --af-tag STRING              Allele frequency tag to use, by default estimated from AN,AC or GT
    -1, --1st-allele-only            Include only 1st allele at multiallelic sites
    -c, --collapse STRING            Treat as identical records with <snps|indels|both|all|some|none>, see man page for details [none]
    -d, --depth INT,INT,INT          Depth distribution: min,max,bin size [0,500,1]
    -e, --exclude EXPR               Exclude sites for which the expression is true (see man page for details)
    -E, --exons FILE.gz              Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, bgzip compressed)
    -f, --apply-filters LIST         Require at least one of the listed FILTER strings (e.g. "PASS,.")
    -F, --fasta-ref FILE             Faidx indexed reference sequence file to determine INDEL context
    -i, --include EXPR               Select sites for which the expression is true (see man page for details)
    -I, --split-by-ID                Collect stats for sites with ID separately (known vs novel)
    -r, --regions REGION             Restrict to comma-separated list of regions
    -R, --regions-file FILE          Restrict to regions listed in a file
        --regions-overlap 0|1|2      Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]
    -s, --samples LIST               List of samples for sample stats, "-" to include all samples
    -S, --samples-file FILE          File of samples to include
    -t, --targets REGION             Similar to -r but streams rather than index-jumps
    -T, --targets-file FILE          Similar to -R but streams rather than index-jumps
        --targets-overlap 0|1|2      Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]
    -u, --user-tstv TAG[:min:max:n]  Collect Ts/Tv stats for any tag using the given binning [0:1:100]
                                       A subfield can be selected as e.g. 'PV4[0]', here the first value of the PV4 tag
        --threads INT                Use multithreading with <int> worker threads [0]
    -v, --verbosity INT              Verbosity level

