frichter / ore Goto Github PK

Various files in the helper_scripts sub-directory contain scripts and wrappers for analyzing GTEx, PCGC, and AMP-AD WGS and RNAseq data. However these need to be formalized and cleaned for a more intuitive walk-through

In the ORE publication you mention that SVs can be tested. What format should an SV be in and how is that format generated? I have tried using lumpy and SV typer to obtain genotypes, but ORE complains "No AD field in FORMAT column". None of my entries contain allelic depth, but they do have DP (read depth). Could DP suffice?

I am not sure if this is a bug in your code handling SVs or if there is a specific SV genotyping tool I should be using to generate the desired information for ORE.

Could you please provide an example of the information required for ORE to accept an SV, and the best way to generate SVs for use in ORE?

Thank you,
Alex

The software outputs are amenable to plotting, but I would like to natively support the ggplot R plots I used to illustrated ORE software outputs in the manuscript (https://doi.org/10.1093/bioinformatics/btz202). Examples:

The current software creates multiple side effect files. These take up space and time through extensive read/write operations. Possible options to explore are HDF5 and/or implementing Python's tempfile module.