bcftools +trio-dnm3 -P samples.ped --use-NAIVE

bcftools +trio-dnm3 -P samples.ped --use-DNG
bcftools +trio-dnm3 -P samples.ped --use-ALM --with-pPL

bcftools +trio-dnm3 -P samples.ped --use-ALM

bcftools +trio-dnm3 -P samples.ped --use-DMM

Usage: bcftools +trio-dnm3 [OPTIONS]
Common options:
   -e, --exclude EXPR              Exclude trios for which the expression is true (one matching sample invalidates a trio)
   -i, --include EXPR              Include trios for which the expression is true (one failing samples invalidates a trio)
   -o, --output FILE               Output file name [stdout]
   -O, --output-type u|b|v|z[0-9]  u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]
   -r, --regions REG               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]
   -t, --targets REG               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]
       --no-version                Do not append version and command line to the header
   -v, --verbosity INT             Verbosity level
   -W, --write-index[=FMT]         Automatically index the output files [off]

General options:
   -m, --min-score NUM             Do not add FMT/DNM annotation if the log score is smaller than NUM
   -p, --pfm [1X:|2X:]P,F,M        Sample names of child (the proband), father, mother; "1X:" for male pattern of chrX inheritance [2X:]
   -P, --ped FILE                  PED file with the columns: <ignored>,proband,father,mother,sex(1:male,2:female)
   -X, --chrX LIST                 List of regions with chrX inheritance pattern or one of the presets: [GRCh37]
                                      GRCh37 .. X:1-60000,chrX:1-60000,X:2699521-154931043,chrX:2699521-154931043
                                      GRCh38 .. X:1-9999,chrX:1-9999,X:2781480-155701381,chrX:2781480-155701381
       --dnm-tag TAG[:type]        Output tag with DNM quality score and its type [DNM:log]
                                       log   .. log-scaled quality (-inf,0; float)
                                       flag  .. is a DNM, implies --use-NAIVE (1; int)
                                       phred .. phred quality (0-255; int)
                                       prob  .. probability (0-1; float)
       --force-AD                  Calculate VAF even if the number of FMT/AD fields is incorrect. Use at your own risk!
       --va TAG                    Output tag name for the variant allele [VA]
       --vaf TAG                   Output tag name for variant allele fraction [VAF]

Models:
       --use-NAIVE                 v0, Naive calling model which uses only FMT/GT to determine DNMs
       --use-DNG                   v1, Original DeNovoGear model, implies --dng-priors
       --use-ALM                   v2, Basic allele-likelihood model (the default until v1.24)
       --use-DMM                   v3, Dirichlet-multinomial model with site noise awareness (the default since v1.24)

Model options:
       --dng-priors                Use the original DeNovoGear priors (including bugs in prior assignment, but with chrX bugs fixed)
       --mrate NUM                 Mutation rate [1e-8]
   -n, --strictly-novel            When Mendelian inheritance is violiated, score highly only novel alleles (e.g. in LoH regions)
       --with-pAD                  Do not use FMT/QS but parental FMT/AD

Model options specific to --use-ALM:
   --ad, --allele-dropout NUM      Mixture weight for missed inherited alleles due to low read depth [0]
         --min-vaf NUM             Baseline variant allele fraction for mosaic scoring, by default off for ALM [0]
   --np, --noise-prior NUM         Prior probability of site-level noise; negative disables multialellic penalty in the child [1e-3]
         --phi NUM                 Dirichlet-multinomial overdispersion for modelling genotypes [1e3]
         --pns FRAC[,NUM][:TYPE]   Maximum allowed parental noise, fraction or number of reads; TYPE is snv, indel, or both;
         --pn  FRAC[,NUM][:TYPE]       --pn is the same as --pns applied for alleles observed in both parents, defaults:
                                       --pns 0.045,0:snv --pn 0.011,0:snv --pns 0:indel --pn 0:indel
   --sb, --strand-bias NUM         Strand bias mixture coefficient; requires FMT/SP [0]
         --with-pPL                Do not use FMT/QS but parental FMT/PL (inflates FDR)

Model options specific to --use-DMM:
         --max-QM NUM              Maximum QM value (phred); negative value to ignore FORMAT/QM annotation [30]
         --min-vaf NUM             Baseline variant allele fraction for mosaic scoring [0.2]
   --np, --noise-prior NUM         Prior probability of site-level noise; negative disables multialellic penalty in the child [1e-3]
         --phi NUM                 Dirichlet-multinomial overdispersion for modelling genotypes [1e3]
         --pns FRAC[,NUM][:TYPE]   See above [--pns 0.045,0:snv --pns 0:indel]
         --pn  FRAC[,NUM][:TYPE]   See above [--pn 0.011,0:snv --pn 0:indel]
   --sb, --strand-bias NUM         Strand bias mixture coefficient; requires FMT/SP [1e-2]

Model options specific to --use-DNG:
   --sb, --strand-bias NUM         Strand bias mixture coefficient; requires FMT/SP [0]

Example:
   # Annotate VCF with FORMAT/DNM, run for a single trio
   bcftools +trio-dnm3 -p proband,father,mother file.bcf

   # Same as above, but read the trio(s) from a PED file
   bcftools +trio-dnm3 -P file.ped file.bcf

   # Same as above plus extract a list of significant DNMs using the bcftools/query command
   bcftools +trio-dnm3 -P file.ped file.bcf -Ou | bcftools query -i'DNM>10' -f'[%CHROM:%POS %SAMPLE %DNM\n]'

   # A complete example with a variant calling step. Note that this is one long
   # command and should be on a single line. Also note that a filtering step is
   # recommended, e.g. by depth and VAF (not shown here):
   bcftools mpileup -a AD,QM,SP -f ref.fa -Ou proband.bam father.bam mother.bam |
       bcftools call -mv -Ou |
       bcftools +trio-dnm3 -p proband,father,mother -Oz -o output.vcf.gz