Plugin trio-dnm2

General

Calling

Tips and Tricks

Plugin trio-dnm2

This plugin can be used to screen variants for possible de-novo mutations in trios (i.e. in samples with parental data available).

The program adds the following annotations:

FORMAT/DNM: posterior probability of the variant being DNM (see --dnm-tag option)
FORMAT/VA: the variant allele given as a 0-based index to REF,ALT alleles (see --va option)
FORMAT/VAF: the fraction of reads supporting the de novo allele (see --vaf option)

There are three calling models are available:

Naive model: This simply looks at sample genotypes (FORMAT/GT) and identifies sites that violate Mendelian inheritance, taking into account sex inheritance patterns on sex chromosomes and in pseudo-autosomal regions. This model is activated as

bcftools +trio-dnm2 -P samples.ped --use-NAIVE

DeNovoGear model: The original DeNovoGear model with fixed bugs (--with-pPL) or with bugs left as is (--use-DNG) This model is activated as

bcftools +trio-dnm2 -P samples.ped --with-pPL
bcftools +trio-dnm2 -P samples.ped --use-DNG

Trio-DNM model: A new calling model which results in a cleaner callset at the cost of decreased sensitivity to parental mosaics. This model is executed by default

bcftools +trio-dnm2 -P samples.ped

For more information and math notes see http://samtools.github.io/bcftools/trio-dnm.pdf

The list of plugin-specific options can be obtained by running bcftools +trio-dnm2, which will print the following usage page:

About: Screen variants for possible de-novo mutations in trios
Usage: bcftools +trio-dnm2 [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

General options:
   -m, --min-score NUM             Do not add FMT/DNM annotation if the 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]

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]
       --pn FRAC[,NUM]             Tolerance to parental noise or mosaicity, given as fraction of QS or number of reads [0.005,0]
       --pns FRAC[,NUM]            Same as --pn but is not applied to alleles observed in both parents (fewer FPs, more FNs) [0.045,0]
       --use-DNG                   The original DeNovoGear model, implies --dng-priors
       --use-NAIVE                 A naive calling model which uses only FMT/GT to determine DNMs
       --with-pAD                  Do not use FMT/QS but parental FMT/AD
       --with-pPL                  Do not use FMT/QS but parental FMT/PL. Equals to DNG with bugs fixed (more FPs, fewer FNs)

Example:
   # Annotate VCF with FORMAT/DNM, run for a single trio
   bcftools +trio-dnm2 -p proband,father,mother file.bcf

   # Same as above, but read the trio(s) from a PED file
   bcftools +trio-dnm2 -P file.ped file.bcf

   # Same as above plus extract a list of significant DNMs using the bcftools/query command
   bcftools +trio-dnm2 -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,QS -f ref.fa -Ou proband.bam father.bam mother.bam |
       bcftools call -mv -Ou |
       bcftools +trio-dnm2 -p proband,father,mother -Oz -o output.vcf.gz

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