Triodenovo

10/03/2017

Triodenovo is working with the joint called VCF from GATK. So, we just do:

../../software/triodenovo.0.05/bin/triodenovo --ped ../9004_trio.ped --in_vcf ../VCF/recalibrated_variants.vcf --out 9004_denovo.vcf

I'll likely have to play with filtering and other parameters (https://genome.sph.umich.edu/wiki/Triodenovo), but for now at least we're getting results.

Then it's just a matter of running it for all trios:

while read t; do ../../software/triodenovo.0.05/bin/triodenovo --ped ../${t}.ped --in_vcf ../VCF/recalibrated_variants.vcf --out ${t}_denovo.vcf; done < ../trio_ids.txt