Recently I keep running bcbio with two whole genome sequence samples with 50X on AWS virtual machine (32 cores + 60GB RAM). It takes 4 days for mutect + scalpel to process 4 chromosomes. I checked the cpu usage of that machine, and mutect+scalpel is using all cpu resource. But when I use bcbio + freebayes or bcbio + varscan to process the same dataset, it only took 20 hours to finish variants calling. I am not sure if there is a way to improve the speed of mutect + scalpel or use mutect + other indel callers.
ghost
commented
10 years ago
Hi Brad,
Recently I keep running bcbio with two whole genome sequence samples with 50X on AWS virtual machine (32 cores + 60GB RAM). It takes 4 days for mutect + scalpel to process 4 chromosomes. I checked the cpu usage of that machine, and mutect+scalpel is using all cpu resource. But when I use bcbio + freebayes or bcbio + varscan to process the same dataset, it only took 20 hours to finish variants calling. I am not sure if there is a way to improve the speed of mutect + scalpel or use mutect + other indel callers.
Thanks, Guorong