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ultimatesource / denovogear

A program to detect denovo-variants using next-generation sequencing data.
http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2611.html
GNU General Public License v3.0
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Denovogear and DenovogearBB #313

Open StellaXia opened 3 years ago

StellaXia commented 3 years ago

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 commented 3 years ago

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