Ensure reference genomes match renee

[kelly-sovacool]

XAVIER/config/genomes/biowulf/hg38.json

Line 11 in 237187c

"GENOME": "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/genome/Homo_sapiens_assembly38.fasta",

renee uses fastas from GDC which include decoys & viruses

[samarth8392]

comment from Vishal:

I see that XAVIER is not using the GDC fasta file

XAVIER/config/genomes/biowulf/hg38.json

Line 11 in 237187c

"GENOME": "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/genome/Homo_sapiens_assembly38.fasta",

...found here --> https://gdc.cancer.gov/about-data/gdc-data-processing/gdc-reference-files.. we are already using the GDC fasta file in our RENEE. I think like GDC we should use the same fasta file for all our processing pipelines. Can XAVIER switch to the GDC fasta?

[kelly-sovacool]

@samarth8392 do you know the commands that need to be run on each fasta to create the various files that xavier needs? We should at least have a bash script to document the process.

[samarth8392]

Unfortunately, I don't. The reason why I haven't worked on this yet is because I have never updated any of the config files. You are absolutely right. We should document how these were created (for both mm10 and hg38) and then we can build and update references.
We would have to reverse engineer it.

[kelly-sovacool]

Just need to switch the fasta file to the GDC reference and ensure the BWA reference exists in the same directory