Dear Biostar Leaders,
I built a exome pipeline with standard tools like fastQC + BWA-MEM align + GATK + samtools + Picard + freebayes + samblaster. My pipeline runs on a local Linux Server(HP) that runs "Red Hat Enterprise Linux 7.3"
Our IT staff has informed me about the recent news on a hardware-memory vulnerability called "Meltdown & Spectre" that affects servers containing Intel microprocessors. RedHat has released some patch upgrades to solve this vulnerability.
ReadHat has also indicated that this upgrade will cause a performance degrade (up to 30%). I am wondering if anyone of you has made similar upgrades and seen any performance hits at various stages of the ngs pipeline ? Which ngs related tools have got affected the most due to this patch upgrade ?
Redhat patch is : https://access.redhat.com/security/vulnerabilities/speculativeexecution?sc_cid=701f2000000tsLNAAY&; The 3 vulnerabilities are : CVE-2017-5754, CVE-2017-5753, & CVE-2017-5715 More information about these vulnerabilities are here : https://www.wired.com/story/meltdown-and-spectre-patches-take-toll/
Thanks, gsr
@genomax, thank you for your answer