Led by Jeffrey Ng of the Turner Lab at Washington University. Please navigate to the various folders to find code for the different parts of the project.
The de novo workflow folder has the scripts required to run the de novo calling workflow.
This folder holds various scripts that were used to run the comparison of the various NA12878 samples. This also holds the general code for how Parabricks, GLnexus, and preprocessing steps were run before running it in the de novo workflow
This folder holds a Snakemake workflow that creates a karyotype for a sample.
This folder holds the codes for running unfazed on de novo calls to get the parent-of-origin chromosome for the de novo variants.
This folder holds the codes for estimating EBV copy number.
While not shown in this Github repo, this analysis was run using deconstructSigs from Parabricks. The version in the Parabricks software program is very similar to the original found here.
Link can be found here
UCSC Genome Browser track for 1000 Genomes Project DNV calls link:
https://data.cyverse.org/dav-anon/iplant/home/turnerlabwashu/Turner_Lab_Track_Hubs/Ng_et_al_1000G_DNV_Paper/hub.txt