Denovogear and DenovogearBB

[StellaXia]

Hi,

It is mentioned in the Denovogear paper that the software implements Denovogear (using SAMTools genotype likelihoods) and DenovogearBB (beta binomial based likelihoods). Actually, I'd like to implement DenovogearBB but not Denovogear.

I'm wondering how to distinguish DenovogearBB with Denovogear, taking the folloing code as an example.

bcftools mpileup -a 'AD,DP'
-r chr8 -f Homo_sapiens_assembly38.fasta
sample1.bam
sample2.bam
sample3.bam |
bcftools call -mv -Ov -o trio8/chr8.vcf

dng-dnm auto --ped trio8/trio8.ped
--vcf trio8/chr8.vcf
--output_vcf trio8/dngout_chr8.vcf

Thank you very much and looking forward to your reply.

[reedacartwright]

I no longer support dng-dnm. You can try using dng-call which uses a dirichlet-multinomial for genotype likelihoods.

[penglbio]

I use denovogear1.1.1 , command like this ，dng dnm auto --ped trio8/trio8.ped
--vcf trio8/chr8.vcf
--output_vcf trio8/dngout_chr8.vcf why all the sites in my output ,the pp_dnm is very small ,little row is >0.2,