Running time when using CRAM input

[mkohailan]

Hi, I tried the latest version of RUFUS to run CRAM files (because the -cr option was not available in the version I have from 2018).

However, the run takes almost a week to finish, while it takes only overnight with BAMs.

Any thoughts on this?

[jandrewrfarrell]

Glad Rufus has been working for you, sorry about the slowdown, there’s definitely something off it shouldn’t take that long. The —cr option should not slow down Rufus that much, all it really does is change the samtools command used to read the files. What type of data are you during, whole genome or exome? Can you send me an example of your command line? ================================= Andrew Farrell PhD Director of Research and Science Department of Human Genetics USTAR Center for Genetic Discovery Eccles Institute of Human Genetics University of Utah School of Medicine​ 15 North 2030 East, Room 7140 Salt Lake City, UT 84112-5330 Email: ***@***.*** http://marthlab.org/ =================================

…

On Aug 7, 2022, at 1:25 AM, mkohailan ***@***.***> wrote:  Hi, I tried the latest version of RUFUS to run CRAM files (because the -cr option was not available in the version I have from 2018). However, the run takes almost a week to finish, while it takes only overnight with BAMs. Any thoughts on this? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.