search

CCBR / LOGAN

https://ccbr.github.io/LOGAN/
MIT License
1 stars 4 forks source link

support optional dragen processor on biowulf #31

Open kelly-sovacool opened 5 months ago

kelly-sovacool commented 5 months ago

Need to add a toggle for gatk (+ bwa + picard) vs dragon (give fastq directly and it handles trim, align, variant calling)

Are we already doing scatter/gather (splitting chromosomes) to speed up processing time with gatk?

kelly-sovacool commented 4 months ago

HPC dragen partition: https://hpc.nih.gov/docs/nci-dragen.html

dnousome commented 4 months ago

Thanks for adding. @kelly-sovacool yes we do scatter and gather to speed up processing times. For GATK, this is at the base quality recalibration step. We also split at the variant calling/CNV/SV level when possible. For Dragen, looks like only certain users will be approved to run at the moment, but definitely we can lay the ground work for the submission. Potential issues I see are the egress to the /staging directory for this Dragen server and also differences between genome builds