Impact on GATK performance due to Vulnerabilities - Meltdown and Spectre ?
Dear GATK Team,
I developed an exome pipeline with standard GATK Best Practices guidelines (BWA-MEM align + Realign + BQSR + HaplotypeCaller). Our pipeline implements GATK 3.7 and it runs on a local Linux Server(HP) that runs "Red Hat Enterprise Linux 7.3"
I was recently informed by our organizational IT staff about the recent news on a hardware-memory vulnerability called "Meltdown & Spectre" that affects servers containing Intel microprocessors. Red Hat team has identified this as an industry-wide issue, and has classified this threat as an "Important Impact" and hence strongly recommends to apply patch release of their BIOS and OS patches.
RedHat has indicated that this patch would possibility cause a performance degrade (up to 30%), hence I am wondering if Broad is encountering this issue ? I am wondering if you have evaluated how much of an impact does this patch upgrade causes on performance of GATK ?
Our IT team wants to apply the following patch
The 3 vulnerabilities are : CVE-2017-5754, CVE-2017-5753, & CVE-2017-5715
More information about these vulnerabilities are here :