Trio

The trio calling model is for calling germline variation and de novo mutations in parent-offspring trios.

Usage

To call germline and de novo mutations in a trio, either specify both maternal (--maternal-sample; -M) and paternal (--paternal-sample; -F) samples:

$ octopus -R hs37d5.fa -I NA12878.bam NA12891.bam NA12892.bam -M NA12892 -F NA12891

or provide a PED file which defines the trio:

$ octopus -R hs37d5.fa -I NA12878.bam NA12891.bam NA12892.bam --pedigree ceu_trio.ped

Setting ploidies

The trio calling model is currently only fully supported for diploid samples. You can set sample contig ploidies with the --contig-ploidies (-p) option:

$ octopus -R hs37d5.fa -I NA12878.bam NA12891.bam NA12892.bam -M NA12892 -F NA12891 -p NA12891:X=1

De novo mutations only

To call only DENOVO mutations, just add the --denovos-only command:

$ octopus -R hs37d5.fa -I NA12878.bam NA12891.bam NA12892.bam --ped ceu_trio.ped --denovos-only

Note this only works for filtered calls, and should only be used if you do not plan on re-filtering the calls, since this will not be possible once the germline mutations are removed.

Performance consideration

Like for the population model, --max-joint-genotypes has a large baring on overall accuracy and runtime. Increasing this parameter can improve sensitivity, but will also result in longer runtimes. The default value is set with accuracy in mind.